Layer selection effect on solid state 13C and 15N chemical shifts calculation using ONIOM approach

Shaghaghi, Hoora; Ebrahimi, Hossein Pasha; Panah, Niloufar Bahrami; Tafazzoli, Mohsen

doi:10.1016/j.ssnmr.2013.01.002

Cited by 9 publications

(3 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, a comparison was made between the theoretically calculated 13 C chemical shift constants and the experimentally measured 13 C chemical shifts. GIAO (Gauge Including Atomic Orbital) as the most widely used approach for calculating NMR shielding tensors were applied [27][28][29][30][31][32][33]. The Gaussian 09 package was employed to perform optimization of structures and all the calculations [34].…”

Section: Computational Aspectsmentioning

confidence: 99%

Spectroscopic, thermal analysis and DFT computational studies of salen-type Schiff base complexes

Ebrahimi

Hadi

Abdulnabi

et al. 2014

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

Self Cite

View full text Add to dashboard Cite

Section: Computational Aspectsmentioning

confidence: 99%

Spectroscopic, thermal analysis and DFT computational studies of salen-type Schiff base complexes

Ebrahimi

Hadi

Abdulnabi

et al. 2014

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

Self Cite

View full text Add to dashboard Cite

“…Based on the observations, we proposed an approach that can graphically differentiate α‐helix from β‐sheet structure with no requirement of highly accurate calculations, priori knowledge of protein structure, structural refinement, or multiple experimental datasets. The hybrid computation method, 2‐layer ONIOM(Our owN n‐layer Integrated molecular Orbital and molecular mechanics Method), was applied to diminish the cost of calculation . To assess whether the proposed approach and amino acids chemical shifts variation is depended on the computational method, NMR shielding tensors were calculated either using Full‐DFT method or ONIOM(DFT‐HF) with different basis set for the high layer.…”

Section: Introductionmentioning

confidence: 99%

A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory

et al. 2016

Self Cite

View full text Add to dashboard Cite

The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of (13) C(α) chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of (13) C(β) , and (1) H(α) chemical shifts nor on the variation of absolute deviation of (13) C(α) chemical shifts relative to ψ dihedral angle. The (13) C(α) absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of highly accurate calculations, priori knowledge of protein structure and structural refinement. Comparison of Full-DFT and ONIOM(DFT:HF) approaches illustrates that the trend of (13) C(α) ADCC plots are independent of computational method but not of basis set valence shell type.

show abstract

“…The primary result of any quantum‐chemical calculation of NMR parameters is the absolute magnetic shielding tensors, which have more physical significance than the chemical shifts. A number of articles have recently appeared in the literature to discuss the accuracy of modest theoretical levels in the prediction of shielding tensors of H, C, N, P, and F nuclei, because these are the greatest important nuclei in NMR experiments and are studied in various molecules .…”

Section: Introductionmentioning

confidence: 99%

Probing theoretical level effect on fluorine chemical shielding calculations

Ebrahimi

Tafazzoli

2013

Concepts Magnetic Resonance

Self Cite

View full text Add to dashboard Cite

The extensive quantum‐chemical calculations are assessed for prediction of the 19F nuclear magnetic shielding constants. The methods within domain of density functional theory (DFT) and ab initio, Hartree–Fock (HF), and second‐order Møller–Plesset perturbation theory (MP2) are employed for calculation of the 19F chemical shielding constants for a series of 30 small fluorine‐containing molecules. The importance of inclusion of four factors, namely, electron correlation treatment, triple‐ξ valence shell, diffuse function, and polarization function on calculating the fluorine NMR chemical shieldings for a variety of Pople's standard basis sets at gauge invariant atomic orbital (GIAO) and continuous set of gauge transformation (CSGT) conditions are discussed by employing the linear regression analysis. The systematic investigation performed here on the influence of the method, level of theory, and basis set size on the accuracy of 19F chemical shielding demonstrates that the presence of a high level of electron correlation factor in level as well as the polarization function in basis set leads to an accurate wave function to compute the reliable fluorine chemical shielding. The results analysis illustrates that the polarization function has a significant effect on the basis sets to minimize the difference between theoretical and experimental values in several fluorine molecules. An additional comparison of the GIAO and CSGT results is used as a supplementary study to confirm the validity of the results. The basis set dependence of fluorine chemical shielding constants verifies that GIAO provides results that are often more accurate than those that are calculated with CSGT approach at the same basis set size, as expected. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 140‐153, 2013.

show abstract

Layer selection effect on solid state 13C and 15N chemical shifts calculation using ONIOM approach

Cited by 9 publications

References 57 publications

Spectroscopic, thermal analysis and DFT computational studies of salen-type Schiff base complexes

Spectroscopic, thermal analysis and DFT computational studies of salen-type Schiff base complexes

A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory

Probing theoretical level effect on fluorine chemical shielding calculations

Contact Info

Product

Resources

About