Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach

2018 ◽  
Vol 20 (20) ◽  
pp. 14003-14012 ◽  
Author(s):  
Q. Nhu N. Nguyen ◽  
Joshua Schwochert ◽  
Dean J. Tantillo ◽  
R. Scott Lokey
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Cyclic Peptide ◽  
Chemical Shifts ◽  
Low Energy ◽  
Functional Prediction ◽  
1H And 13C Nmr ◽  
New Approach ◽  
Solution Structures ◽  
Peptide Conformations

Conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), a new approach for determining solution structures.

scholarly journals Structural and spectroscopic characterization and DFT studies of 2-amino-1,10-phenanthrolin-1-ium chloride

2019 ◽  
Vol 10 (2) ◽  
pp. 95-101
Author(s):  
Sebile Işık Büyükekşi ◽  
Namık Özdemir ◽  
Abdurrahman Şengül
Keyword(s):  
Density Functional Theory ◽  
Electronic Absorption ◽  
13C Nmr ◽  
Density Functional ◽  
Electronic Absorption Spectra ◽  
Chemical Shifts ◽  
Atomic Orbital ◽  
Basis Set ◽  
Functional Theory ◽  
1H And 13C Nmr

A versatile synthetic building block, 2-amino-1,10-phenanthrolin-1-ium chloride (L∙HCl) was synthesized and characterized by IR, 1H and 13C NMR DEPT analysis, UV/Vis and single-crystal X-ray diffraction technique. The molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO), 1H and 13C NMR chemical shifts values of the title compound in the ground state were obtained by using density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set and compared with the experimental data. Electronic absorption spectrum of the salt was determined using the time-dependent density functional theory (TD-DFT) method at the same level. In the NMR and electronic absorption spectra calculations, the effect of solvent on the theoretical parameters was included using the default model with DMSO as solvent. The obtained theoretical parameters agree well with the experimental findings.

scholarly journals A theoretical investigation on the isomerism and the NMR properties of thiosemicarbazones

2007 ◽  
Vol 5 (2) ◽  
pp. 396-419 ◽  
Author(s):  
N. Nuwan De Silva ◽  
Titus Albu
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Intermolecular Hydrogen Bond ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
1H And 13C Nmr ◽  
Nmr Characterization ◽  
Hybrid Density Functional ◽  
Nmr Properties

AbstractHybrid density functional theory calculations at the mPW1PW91/6-31+G(d,p) level of theory have been used to investigate the optimized structures and other molecular properties of five different series of thiosemicarbazones. The investigated compounds were obtained from acenaphthenequinone, isatin and its derivatives, and alloxan. The focus of the study is the isomerism and the NMR characterization of these thiosemicarbazones. It was found that only one isomer is expected for thiosemicarbazones and methylthiosemicarbazones, while for dimethylthiosemicarbazones, two isomers are possible. All investigated thiosemicarbazones exhibit a hydrazinic proton that is highly deshielded and resonates far downfield in the proton NMR spectra. This proton is a part of a characteristic sixmembered ring, and its NMR properties are a result of its strong, intermolecular hydrogen bond. The relationships between the calculated 1H and 13C NMR chemical shifts and various geometric parameters are reported.

scholarly journals Hybrid density functional theory investigation of a series of alloxan-based thiosemicarbazones and semicarbazones

2006 ◽  
Vol 4 (4) ◽  
Author(s):  
N. Nuwan De Silva ◽  
Edward Lisic ◽  
Titus Albu
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Functional Theory ◽  
1H And 13C Nmr ◽  
Hydrogen Bond Interactions ◽  
Linear Relationships ◽  
Nmr Characterization ◽  
The Relationship ◽  
Hybrid Density Functional

AbstractRecently, the synthesis and the NMR characterization of a series of eight alloxan-based thiosemicarbazones and semicarbazones were reported. These compounds exhibit a strongly hydrogenbonded hydrazinic proton that is a part of a characteristic six-membered ring. This proton is highly deshielded and resonates far downfield in the proton NMR spectra. In this report, mPW1PW91/6-31+G(d,p) calculations have been used to investigate the structure and other molecular properties of this series of eight compounds. The relationship between the 1H and 13C NMR chemical shifts and various geometric parameters was investigated, and linear relationships for proton peaks that are involved in hydrogen-bond interactions were found.

scholarly journals Substituent Effects on NMR Spectroscopy of 2,2-Dimethylchroman-4-one Derivatives: Experimental and Theoretical Studies

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2061
Author(s):  
Daniela Iguchi ◽  
Davide Ravelli ◽  
Rosa Erra-Balsells ◽  
Sergio M. Bonesi
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Substituent Effects ◽  
Heterocyclic Ring ◽  
Functional Theory ◽  
1H And 13C Nmr ◽  
Meta Position ◽  
Experimental And Theoretical Studies ◽  
Nmr Signals ◽  
C Nmr

The attribution of 1H and 13C NMR signals of a library of 5-, 6- and 7-substituted 2,2-dimethylchroman-4-one derivatives is reported. Substituent effects were interpreted in terms of the Hammett equation, showing a good correlation for carbons para- to the substituent group, not for the meta- ones. Similarly, the Lynch correlation shows the additivity of the substituent chemical shifts in the case of both H and C nuclei, again with the exception of the carbons in the meta- position. Density Functional Theory (DFT)-predicted 1H and 13C chemical shifts correspond closely with experimentally observed values, with some exceptions for C NMR data; however, the correlation is valid only for the aromatic moiety and cannot be extended to the heterocyclic ring of the chroman-4-one scaffold.

scholarly journals Density functional theory: 1H and 13C-NMR spectra of some coumarin derivatives

2014 ◽  
Vol 79 (11) ◽  
pp. 1405-1411 ◽  
Author(s):  
Selma Spirtovic-Halilovic ◽  
Mirsada Salihovic ◽  
Snezana Trifunovic ◽  
Suncica Roca ◽  
Elma Veljovic ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
13C Nmr ◽  
Density Functional ◽  
Nmr Spectra ◽  
Chemical Shifts ◽  
13C Nmr Spectra ◽  
Coumarin Derivatives ◽  
Functional Theory ◽  
1H And 13C Nmr ◽  
Isotropic Chemical Shifts

For some synthesized coumarin derivatives, 1H and 13C NMR isotropic chemical shifts and some other molecular properties were calculated using density functional theory. The calculations yield reliable results, that are in good correlation with experimental data. This is a good basis for the collaboration between experimentalists and quantum chemists.

scholarly journals The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

IUCrJ ◽  
2017 ◽  
Vol 4 (2) ◽  
pp. 175-184 ◽  
Author(s):  
Xiaozhou Li ◽  
Marcus A. Neumann ◽  
Jacco van de Streek
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Force Field ◽  
Solid State Nmr ◽  
Density Functional ◽  
Chemical Shifts ◽  
Density Functional Theory Calculations ◽  
Free Base ◽  
Nmr Crystallography

Motional averaging has been proven to be significant in predicting the chemical shifts inab initiosolid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations.

scholarly journals A New Approach Using Aromatic-Solvent-Induced Shifts in NMR Spectroscopy to Analyze β-Lactams with Various Substitution Patterns

Synlett ◽  
2019 ◽  
Vol 31 (02) ◽  
pp. 158-164 ◽  
Author(s):  
Leticia Chavelas-Hernández ◽  
Jonathan R. Valdéz-Camacho ◽  
Luis G. Hernández-Vázquez ◽  
Blanca E. Dominguez-Mendoza ◽  
María G. Vasquez-Ríos ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Nmr Spectroscopy ◽  
1H Nmr Spectroscopy ◽  
Density Functional ◽  
Chemical Shifts ◽  
Density Functional Theory Calculations ◽  
Aromatic Solvent ◽  
Functional Theory ◽  
New Approach ◽  
Lactam Ring

The chemical shifts of protons depend not only on the properties of the solute molecule but also on the medium in which the solute resides. A series of β-lactams with various substitution patterns were synthesized to study aromatic-solvent-induced shifts (ASISs) in chloroform and benzene by using 1H NMR spectroscopy. The results agreed with those obtained by theoretical density functional theory calculations. The protons of the β-lactam ring are the most affected by the ASIS effect, and they tend to overlap due to the anisotropic effect of benzene.

Density functional theory investigation of the stereochemistry effects on 1H and 13C NMR chemical shifts of poly(vinyl chloride) oligomers

2005 ◽  
Vol 411 (1-3) ◽  
pp. 207-213 ◽  
Author(s):  
Philippe d’Antuono ◽  
Edith Botek ◽  
Benoît Champagne ◽  
Joris Wieme ◽  
Marie-Françoise Reyniers ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Vinyl Chloride ◽  
13C Nmr ◽  
Density Functional ◽  
Chemical Shifts ◽  
Functional Theory ◽  
1H And 13C Nmr ◽  
Nmr Chemical Shifts ◽  
13C Nmr Chemical Shifts ◽  
Poly Vinyl Chloride
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