Studies of structure and dynamics in a nominally symmetric twisted amide by NMR and electronic structure calculations

2006 ◽  
Vol 84 (3) ◽  
pp. 421-428 ◽  
Author(s):  
Alex D Bain ◽  
Hao Chen ◽  
Paul H.M Harrison
Keyword(s):  
Electronic Structure ◽  
Nmr Spectra ◽  
Chemical Exchange ◽  
Electronic Structure Calculations ◽  
Amide Bond ◽  
Electronic Effects ◽  
H Nmr ◽  
Line Shape Analysis ◽  
Structure Calculations ◽  
C Nmr

Amides that are twisted around the C—N bond show unusual spectroscopy and reactivity when compared with planar amides. The diacyl derivatives of 3,4,7,8-tetramethyl-2,5-dithioglycoluril are intriguing examples of this class, since the crystal structures show that the two acyl groups are twisted by different amounts on either side of the molecule owing to a combination of steric and electronic effects. However, the 1H NMR spectra in solution at room temperature exhibit only one acyl resonance, so there must be fast interconversion among pairs of equivalent structures of each compound. We have prepared a number of derivatives with different acyl groups, both on the glycoluril framework as well as on its dithio analogue. The chemical exchange in solution was slowed down sufficiently by cooling to see individual sites for only two compounds: the dithiodipivaloyl and the dithiodiadamantyl derivatives. The barriers were estimated at 41 kJ mol–1 for the dipivaloyl derivative and 45 kJ mol–1 for diadamantyl derivative. The results show that rotation around the twisted amide bond is slowed by both the steric size of the acyl group and the presence of the thioureido group vs. the ureido group in the glycoluril core. In the solid-state 13C NMR spectra, there is no evidence for any dynamics, even for the diacetyl derivative at ambient temperature. Electronic structure calculations predict a geometry for the dipivaloyl derivative very close to that observed in the crystal structure. These results indicate that the crystal confines, but does not distort the molecule. A mechanism for the exchange is proposed. The relevance of these results to the mechanism of Claisen-like condensations in diacylglycolurils is also discussed.Key words: 1H and 13C NMR, exchange, dynamics, CP/MAS, solids, line shape analysis, amides, twisted amides, atropisomers, glycoluril.

Electronic structure of low-spin six-coordinate iron(III) meso-tetrapropylchlorin complexes

2014 ◽  
Vol 18 (08n09) ◽  
pp. 778-791 ◽  
Author(s):  
Akira Ikezaki ◽  
Jyunpei Ono ◽  
Yoshiki Ohgo ◽  
Mari Fukagawa ◽  
Takahisa Ikeue ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Ground State ◽  
Nmr Spectra ◽  
Spectroscopic Properties ◽  
H Nmr ◽  
Axial Ligands ◽  
Splitting Parameter ◽  
Nmr Signals ◽  
Electronic Ground ◽  
C Nmr

Low-spin iron(III) tetrapropylchlorins [ Fe ( T n PrC ) L 2]± (L = HIm, 1-MeIm, DMAP, CN-, 4-CNPy, tBuNC) adopt the dxy-type ground state regardless of the nature of axial ligands. Among the complexes examined, [ Fe ( T n PrC )( t BuNC )2]+ has shown quite unique spectroscopic properties as described below. (1) 1 H NMR signals were extremely broad as compared with those of other complexes. In particular, 5,20- CH 2(α) signal was too broad to detect. (2) No signals except C γ were observed in 13 C NMR spectra. (3) Tetragonal splitting parameter (|Δ|) estimated by the EPR g values at 4.2 K reached as much as 12.4 λ, which is the largest |Δ| value among all the low-spin iron(III) porphyrins and porphyrinoids reported previously. On the basis of these results, we have concluded that [ Fe ( T n PrC )( t BuNC )2]+ adopts the low-spin iron(III) with (dxz, dyz)4(dxy)1 electronic ground state at 4.2–30 K where the EPR spectra are taken, while it should be expressed as the low-spin Fe ( II ) chlorin π-radical cation [ Fe II ( T n PrC .)( t BuNC )2]+ at ambient temperature where the NMR spectra are taken.

Conformational Structure of N-Methyl-8-octanelactam and Poly(N-methyl-8-octanelactam) as Studied by NMR, Infrared and Raman Spectroscopy and by Theoretical Calculations

1995 ◽  
Vol 60 (11) ◽  
pp. 1798-1808
Author(s):  
Jiří Dybal ◽  
Danica Doskočilová ◽  
Bohdan Schneider ◽  
Rudolf Puffr
Keyword(s):  
Nmr Spectra ◽  
Theoretical Calculations ◽  
Amide Bond ◽  
Conformational Structure ◽  
H Nmr ◽  
Infrared And Raman Spectroscopy ◽  
Stable Forms ◽  
Cis And Trans ◽  
Structure In Solution ◽  
C Nmr

It was proved by 1H and 13C NMR spectra that in N-methyl-8-octanelactam in CDCl3 solution, the amide bond assumes only the cis form. Mirror inversion about the plane of the amide bond occurs with an activation enthalpy ∆H# = 44.7 kJ/mol. Molecular mechanics and quantum mechanical calculations yielded four favoured conformational structures for the isolated molecule. By vibrational spectra, one of two distinguishable structures strongly predominates. From 1H NMR spectra, this predominant conformation was identified with one of the calculated stable forms. By 13C NMR evidence, poly(N-methyl-8-octanelactam) in tetrachloroethane solution contains equal populations of the cis and trans amide forms; the structure of this polymer in the rubbery solid state seems to be similar to its structure in solution.

scholarly journals Demystifying fluorine chemical shifts: electronic structure calculations address origins of seemingly anomalous 19F-NMR spectra of fluorohistidine isomers and analogues

2015 ◽  
Vol 17 (45) ◽  
pp. 30606-30612 ◽  
Author(s):  
Chandana Kasireddy ◽  
James G. Bann ◽  
Katie R. Mitchell-Koch
Keyword(s):  
Electronic Structure ◽  
Chemical Shift ◽  
Electron Density ◽  
Nmr Spectra ◽  
Chemical Shifts ◽  
Electronic Structure Calculations ◽  
19F Nmr ◽  
19F Nmr Spectra ◽  
Structure Calculations

Understanding localization/delocalization of fluorine electron density is shown to be critical for predicting and interpreting fluorine chemical shift.

Identification and computational characterization of isomers with cis and trans amide bonds in folate and its analogues

2018 ◽  
Vol 20 (45) ◽  
pp. 28818-28831 ◽  
Author(s):  
Stoyan Iliev ◽  
Gergana Gocheva ◽  
Nikoleta Ivanova ◽  
Boyana Atanasova ◽  
Jasmina Petrova ◽  
...  
Keyword(s):  
Electronic Structure ◽  
First Principles ◽  
Md Simulations ◽  
Electronic Structure Calculations ◽  
Amide Bond ◽  
Amide Bonds ◽  
Cis And Trans ◽  
Configurational Isomerism ◽  
Structure Calculations

MD simulations and first-principles electronic structure calculations reveal viable configurational isomerism of a peptide-like amide bond in folate and its analogues.

X-ray structural and nuclear magnetic resonance study of open chain and macrocyclic thioether complexes

1990 ◽  
Vol 68 (8) ◽  
pp. 1357-1363 ◽  
Author(s):  
C. Robert Lucas ◽  
Shuang Liu ◽  
Michael J. Newlands ◽  
Eric J. Gabe
Keyword(s):  
Nmr Spectra ◽  
Chemical Exchange ◽  
Variable Temperature ◽  
Low Frequency ◽  
Nuclear Magnetic Resonance Study ◽  
Conformational Exchange ◽  
Open Chain ◽  
H Nmr ◽  
Chain Complexes ◽  
C Nmr

Preparations of the thiophenophane and open chain thioether complexes MX2•BBTE(M = Pd; X = Cl, I)(M = Pt; X = Cl) (BBTE = 1,2-bis(benzylthio)ethane) and MX2•L (M = Pd; X = Cl, Br, I, SCN) (M = Pt; X = Cl) (L = 2,5,8-trithia[9](2,5)thiophenophane) are described. The molecular structure of PdBr2•L which contains a weak thiophene-sulfur-to-palladium interaction has been determined: space group P21/n, a = 8.3569(3), b = 16.3254(15), c = 11.1462(3) Å, β = 92.833(4)°, Z = 4, Rf = 0.060, Rw = 0.058. The electronic, low frequency ir, and 13C nmr spectra are described. Variable temperature 1H nmr spectra are discussed and it is concluded that the open chain complexes undergo rapid conformational exchange at room temperature but are configurationally rigid unless the temperature is increased. In contrast, the macrocyclic complexes undergo very limited conformational and no configurational exchange up to their decomposition temperatures. They are also nonfluxional in the same temperature range. Chemical exchange of acidic ligand hydrogens and a metal–ligand dissociative equilibrium were also detected when X = SCN. Keywords: thiophene, thioether, macrocyclic metal complexes.

Solvent Effects on Chemical Exchange in a Push–Pull Ethylene as Studied by NMR and Electronic Structure Calculations

2011 ◽  
Vol 115 (26) ◽  
pp. 7531-7537 ◽  
Author(s):  
Maysoon Ababneh-Khasawneh ◽  
Blythe E. Fortier-McGill ◽  
Marzia E. Occhionorelli ◽  
Alex D. Bain
Keyword(s):  
Electronic Structure ◽  
Solvent Effects ◽  
Chemical Exchange ◽  
Electronic Structure Calculations ◽  
Structure Calculations

Message Passing Neural Networks for Partial Charge Assignment to Metal-Organic Frameworks

2020 ◽  
Author(s):  
Ali Raza ◽  
Arni Sturluson ◽  
Cory Simon ◽  
Xiaoli Fern
Keyword(s):  
Electronic Structure ◽  
Message Passing ◽  
Gas Adsorption ◽  
Metal Organic Frameworks ◽  
Computational Cost ◽  
Electronic Structure Calculations ◽  
High Fidelity ◽  
Partial Charges ◽  
Metal Organic ◽  
Structure Calculations

Virtual screenings can accelerate and reduce the cost of discovering metal-organic frameworks (MOFs) for their applications in gas storage, separation, and sensing. In molecular simulations of gas adsorption/diffusion in MOFs, the adsorbate-MOF electrostatic interaction is typically modeled by placing partial point charges on the atoms of the MOF. For the virtual screening of large libraries of MOFs, it is critical to develop computationally inexpensive methods to assign atomic partial charges to MOFs that accurately reproduce the electrostatic potential in their pores. Herein, we design and train a message passing neural network (MPNN) to predict the atomic partial charges on MOFs under a charge neutral constraint. A set of ca. 2,250 MOFs labeled with high-fidelity partial charges, derived from periodic electronic structure calculations, serves as training examples. In an end-to-end manner, from charge-labeled crystal graphs representing MOFs, our MPNN machine-learns features of the local bonding environments of the atoms and learns to predict partial atomic charges from these features. Our trained MPNN assigns high-fidelity partial point charges to MOFs with orders of magnitude lower computational cost than electronic structure calculations. To enhance the accuracy of virtual screenings of large libraries of MOFs for their adsorption-based applications, we make our trained MPNN model and MPNN-charge-assigned computation-ready, experimental MOF structures publicly available.<br>

Conformational structure of ethylene glycol dibenzoate. Vibrational and NMR spectra

1981 ◽  
Vol 46 (8) ◽  
pp. 1913-1929 ◽  
Author(s):  
Bohdan Schneider ◽  
Pavel Sedláček ◽  
Jan Štokr ◽  
Danica Doskočilová ◽  
Jan Lövy
Keyword(s):  
Ethylene Glycol ◽  
Vibrational Spectra ◽  
Nmr Spectra ◽  
Coupling Constants ◽  
Conformational Structure ◽  
Infrared And Raman Spectra ◽  
H Nmr ◽  
Liquid States ◽  
Crystalline Forms ◽  
C Nmr

It was found that three crystalline forms of ethylene glycol dibenzoate can be prepared. Infrared and Raman spectra of these three forms, as well as of the glassy and liquid states, were measured. From 3JHH coupling constants obtained by analysis of the 13C satellite band of the -CH2- group in 1H NMR spectra, and from the 3JCH coupling constants of the -CO.O.CH2- fragment obtained by analysis of the carbonyl band in 13C NMR spectra it was found that in the liquid state the -CH2-CH2- group exists predominantly in the gauche conformational structure, and the bonds C-O-C-C assume predominantly a trans orientation. The results of the analysis of NMR and vibrational spectra were used for the structural interpretation of conformationally sensitive bands in vibrational spectra of ethylene glycol dibenzoate.

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