Conformational preferences of fluorocyclohexane and 1-fluoro-1-silacyclohexane molecules: ab initio study and NBO analysis

Belyakov, A. V.; Баскаков, А. А.; Ivanov, Anatolii D.; Гарабаджиу, А. В.; Arnason, Ingvar

doi:10.1007/s11224-013-0202-8

Cited by 8 publications

(3 citation statements)

References 32 publications

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“…To ensure that this axial preference can be asserted as the gauche effect, we compared these rings with fluorocyclohexane and 3‐fluoro‐1,1‐dimethyl‐cyclohexane. Similar to other monosubstituted cyclohexanes, fluorocyclohexane and 3‐fluoro‐1,1‐dimethyl‐cyclohexane are preferred in the equatorial conformation (0.19 and 0.61 kcal mol −1 more stable than the axial conformer, respectively), which agrees with a previous report [27] . Therefore, the behaviour found in their phosphorus analogues 3 and 4 can be characterized as a strong gauche effect.…”

Section: Resultssupporting

confidence: 90%

Theoretical and X‐Ray Evidence of Electrostatic Phosphonium anti and gauche Effects

et al. 2022

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Sulphur, not phosphorus, is the only known third‐row element capable of experiencing an electrostatic gauche effect with fluorine. Some six‐membered rings containing an endocyclic phosphorus atom and a β‐fluorine substituent that can interconvert to axial (gauche relative to phosphorus) and equatorial positions were then analysed. While phosphines do not establish an electrostatic attraction between fluorine and phosphorus, some oxidised forms exhibit surprising stability for the sterically disfavoured axial orientation. Because the nature of this behaviour was not obvious, since an intramolecular hydrogen bond can appear, a phosphonium derivative was further studied and its axial conformation was found to be highly stable. A preference for the gauche arrangement appears even for the acyclic and sterically hindered (2‐fluoroethyl)triphenylphosphonium cation. On the other hand, (ethane‐1,2‐diyl)bis(phosphonium) cations are exclusively in anti conformation due to an (+/+)‐electrostatic repulsion between the positively charged phosphonium groups.

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Section: Resultssupporting

confidence: 90%

Theoretical and X‐Ray Evidence of Electrostatic Phosphonium anti and gauche Effects

et al. 2022

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“…For groups with heteroatoms, X = N, O, F, Cl, electrostatic interactions stabilizing the gauche conformation in 1-fluoropropane or 1-propanol (Figs. 7 , 12 ) are expected to stabilize also the axial conformation over equatorial [ 179 ]. Since the experimental data show that the equatorial conformer is the most stable in these cases [ 143 ], the previous effects dominate.…”

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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“…Belyakov et al [33] used natural bond orbital (NBO) and Møller-Plesset perturbation (MP) theory to establish differences in axial and equatorial conformers of fluorocyclohexane and 1-fluoro-1-silacyclohexane (H 2 C(CH 2-CH 2 ) 2 XH-F (X = C or Si). The as-calculated compounds consist of a mixture of conformers with chair conformation and C s symmetry differing in the axial and equatorial positions of the C-F/Si-F bonds, corresponding to a free energy difference of A = (Gax -Geq) = 0.80/ -0.54 kJ mol -1 for X = C/Si.…”

Section: Issuementioning

confidence: 99%

Interplay of thermochemistry and structural chemistry, the journal (volume 24, 2013, issues 3–4) and the discipline

et al. 2014

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The contents of issues 3 and 4 for the calendar year 2013 are summarized in the current review of the journal Structural Chemistry. A brief thermochemical commentary is added to the summary of each paper. Abbreviations AIM Atoms in molecules BNNT Boron nitride nanotube CNC Carbon nanocone CSD Crystal structure determination DFT Density functional theory DNB 1,5-Dinitrobiuret EDA Energy decomposition analysis HF Hartree-Fock GED Gas electron diffraction GIAO Gauge-independent atomic orbital HOMA Harmonic oscillator measure of aromaticity MD Molecular dynamics MP Møller-Plesset perturbation MP2Second-order Møller-Plesset perturbation NRT Natural resonance theory ONIOM Our own N-layered integrated molecular orbital and molecular mechanics QTAIM Quantum theory of atoms-in-molecules NAO Natural atomic orbital NBO Natural bond orbital PES Potential energy surface

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Conformational preferences of fluorocyclohexane and 1-fluoro-1-silacyclohexane molecules: ab initio study and NBO analysis

Cited by 8 publications

References 32 publications

Theoretical and X‐Ray Evidence of Electrostatic Phosphonium anti and gauche Effects

Theoretical and X‐Ray Evidence of Electrostatic Phosphonium anti and gauche Effects

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

Interplay of thermochemistry and structural chemistry, the journal (volume 24, 2013, issues 3–4) and the discipline

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