Complete basis set, hybrid-DFT study and NBO interpretation of conformational analysis of 2-methoxytetrahydropyran and its thiopyran and selenopyran analogues in relation to the anomeric effect

Kasaei, Gholam Abbas; Nori‐Shargh, Davood; Yahyaei, Hooriye; Mousavi, Seiedeh Negar; Pourdavoodi, Elham

doi:10.1080/08927022.2012.683527

Cited by 7 publications

(7 citation statements)

References 53 publications

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“…Because of the anometic effect [ 264 ], the axial conformation of 2-methoxytetrahydropyran and 2-fluorotetrahydropyran is favoured by 1.27 and 2.45 kcal mol −1 , respectively, over the equatorial according to the accurate CCSD(T)/aug-cc-pVDZ//MP2/6-311G(2df,2pd) calculations [ 265 ]. The conformational preferences of 2-methoxytetrahydropyran have been investigated using Dynamic NMR [ 266 ] and calculations [ 267 – 269 ] and for 2-fluorotetrahydropyran experimental and calculated 1 J C-F values and conformational energy calculations have been used [ 270 – 272 ] and calculations. Our DLPNO-CCSD(T) calculations show this difference to be 1.21 and 2.43 kcal mol −1 , respectively.…”

Section: Resultsmentioning

confidence: 99%

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

Stylianakis,

Zervos,

Lii

et al. 2023

J Comput Aided Mol Des

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We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger’s force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree–Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol−1), followed by B3LYP (0.69 kcal mol−1) and the HF theories (0.81–1.0 kcal mol−1). As regards the force fields, the lowest errors were observed for the Allinger’s force fields MM3-00 (1.28 kcal mol−1), ΜΜ3-96 (1.40 kcal mol−1) and the Halgren’s MMFF94 force field (1.30 kcal mol−1) and then for the MM2-91 clones MMX (1.77 kcal mol−1) and MM+ (2.01 kcal mol−1) and MM4 (2.05 kcal mol−1). The DREIDING (3.63 kcal mol−1) and UFF (3.77 kcal mol−1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization. Graphical abstract

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Section: Resultsmentioning

confidence: 99%

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

Stylianakis,

Zervos,

Lii

et al. 2023

J Comput Aided Mol Des

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“…Kasaei et al collected some experimental values from the literature in the range from 0.4 kcal mol −1 to 0.9 kcal mol −1 . 27 They predicted Δ G value of 0.99 kcal mol −1 for MTHP in the gas phase using the CBS-4 method. 27 This Δ G is comparable with the MP2/ΔG/ZPE/aug-cc-pVTZ calculated value of 0.92 kcal mol −1 .…”

Section: Resultsmentioning

confidence: 99%

“…27 They predicted Δ G value of 0.99 kcal mol −1 for MTHP in the gas phase using the CBS-4 method. 27 This Δ G is comparable with the MP2/ΔG/ZPE/aug-cc-pVTZ calculated value of 0.92 kcal mol −1 . For MT his CBS-4 calculated value of 1.92 kcal mol −1 is also comparable to 2.09 kcal mol −1 calculated at the MP2/ΔG/ZPE/aug-cc-pVTZ level of theory.…”

Section: Resultsmentioning

confidence: 99%

“…[9][10][11][12][13][14] The quantitative estimation of the anomeric and exo anomeric effects was made by ab initio and DFT calculations on 2-substituted tetrahydropyran (2-oxane) derivatives as cyclic carbohydrate models. 7,[15][16][17][18][19][20][21][22][23][24][25][26][27] The calculations showed that the strength of the anomeric effect depends on the character of the substituent and decreases in the order: Cl 4 F 4 OCH 3 4 SCH 3 4 OH. Similarly, calculations predicted that the exo anomeric effect diminishes in the order: OCH 3 4 NHCH 3 4 OH 4 SCH 3 .…”

Section: Introductionmentioning

confidence: 99%

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Ab initio modelling of the anomeric and exo anomeric effects in 2-methoxytetrahydropyran and 2-methoxythiane corrected for intramolecular BSSE

Sládek

Holka

Tvaroŝka

2015

Phys. Chem. Chem. Phys.

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Accurate ab initio calculations including basis set limit (BSL) extrapolations, removal of intramolecular basis set superposition error (BSSE), solvent effect corrections, and thermal effects have been carried out to compare the structure and the anomeric and exo-anomeric effect in 2-methoxytetrahydropyran and 2-methoxythiane. The effect of intramolecular BSSE on the energetics was outlined for the first time in these types of compounds. It was found that both title compounds show comparable behaviour with respect to BSSE. The energy gap between the axial and equatorial form of 2-methoxythiane is reduced by 0.23 kcal mol(-1) due to the BSSE correction at the MP2/aug-cc-pVTZ level of theory, and in 2-methoxytetrahydropyran it is reduced by 0.21 kcal mol(-1). The intramolecular BSSE influenced also the energy differences between the gauche and trans conformers in both compounds. Energy decomposition analysis (EDA) reveals that the dominant destabilising interaction is repulsion and its primary stabilizing counterpart is the polarization interaction.

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“…NBO calculations provides a reasonable picture from the structural, energetic, bonding and stereo electronic points of view 31 . DFT level computation is used to investigate the various second-order inter-actions between the filled orbitals of one subsystem and vacant orbital of another subsystem 32 .…”

Section: Natural Bond Orbital (Nbo) Analysismentioning

confidence: 99%

A DFT Investigation of Tris-(4´-(Amino)(1,1´-biphenyl)-3,4-diol) Fe(III) Complex

Matin

Aziz

Islam

2018

Dhaka Univ. J. Sci.

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Phenolic compounds, known as the pyrocatechol act as a metal chelating agent. Molecular details of cross-linking of pyrocatechol by transition metal ions are largely unknown. In the present study, the molecular properties of the tris-(4´-(amino)(1,1´-biphenyl)-3,4-diol)- Fe(III) complex have been investigated using density functional theory (DFT) at 6-311G(d,p). Calculated molecular properties of the optimized structure, the binding energies and spectroscopic properties are compared with the available experimental results. For the tris-complex investigated, the binding of Fe (III) with the catechol derivative is not as strong as the binding of other metal ions with catechol. The IR stretching bands show that the strong IR intensities is due to large charge polarization. Calculated electronic band gap is 2.45 eV which is in the range of transition metal ion-tris-(4´-(amino)(1,1´-biphenyl)-3,4-diol) complexes. The metal-ligand binding energy is 513.54 kcal mol-1, which could be used in understanding the speciation of Fe(III)-catechol complex. Structural parameters obtained from the DFT calculations are in good agreement with the crystallographic data. Dhaka Univ. J. Sci. 66(1): 67-71, 2018 (January)

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Complete basis set, hybrid-DFT study and NBO interpretation of conformational analysis of 2-methoxytetrahydropyran and its thiopyran and selenopyran analogues in relation to the anomeric effect

Cited by 7 publications

References 53 publications

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

Ab initio modelling of the anomeric and exo anomeric effects in 2-methoxytetrahydropyran and 2-methoxythiane corrected for intramolecular BSSE

A DFT Investigation of Tris-(4´-(Amino)(1,1´-biphenyl)-3,4-diol) Fe(III) Complex

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