Study of minimum energy conformers of N-substituted derivatives of piperidine and pyrrolidine. Evidence of weak H-bonding by theoretical correlation with experimental NMR data (original) (raw)
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Journal of Physical Chemistry A, 2007
The log K 1 value of analytical quality was obtained for the NiNTPA complex using the density functional theory (DFT)computed (at the B3LYP/6-311þþG(d,p) level of theory in solvent, CPCM/UAKS) G(aq) values of the lowest-energy conformers of the ligands, nitrilotriacetic acid (NTA) and nitrilotri-3-propanoic acid (NTPA), and the Ni(II) complexes (NiNTA and NiNTPA). The described mathematical protocol is of a general nature. The topological analysis, based on the quantum theory of atoms in molecules (QTAIM) of Bader, was used to characterize coordination bonds, chelating rings, and additional intramolecular interactions in the complexes. The topological data, but not the structural analysis, explained the observed difference in stability of the NiNTA and NiNTPA complexes. It was found that the structural H 3 3 3 H contacts (classically regarded H-clashes, a steric hindrance destabilizing the complex) are in fact the H-H bonds contributing to the overall stability of NiNTPA. Also a CH-O bond was found in NiNTPA. The absence of intramolecular bonds between the atoms that fulfill a distance criterion in NiNTPA is explained by the formation of adjacent intramolecular rings that have larger electron density at the ring critical points when compared with the rings containing these atoms. It is postulated that the strength of a chelating ring (a chelating effect) can be measured by the electron density at the ring critical point. It was found that the strain energy, E s , in the as-in-complex NTPA ligand (E s is significantly lowered by the presence of the intramolecular bonded interactions found by QTAIM) is responsible for the decrease in strength of NiNTPA; the E s ratio (NTPA/NTA) of 1.9 correlates well with the experimental log K 1 ratio (NTA/NTPA) of 1.98.
Journal of Molecular Structure, 2011
Complete conformational analyses of all possible keto and enol forms, molecular structure, intramolecular hydrogen bonding (IHB), and vibrational frequencies of 5,5-dimethyl hexane-2,4-dione (DMHD, also known as acetylpinacolin and pivalylacetone), were investigated by means of ab initio calculations and IR and Raman spectroscopies. The results are compared with those of acetylacetone (AA) and 2,2,6,6-tetramethyl-3,5-heptanedione (TMHD). The energy differences between three stable E1, E2, and E3 chelated enol forms are negligible. Comparing the calculated and experimental band frequencies and intensities suggests the coexisting of these three conformers in comparable proportions in the sample. The vibrational frequencies of DMHD and its deuterated analogue were also clearly assigned. According to the theoretical calculations, the stable cis-enol conformers of DMHD have an average hydrogen bond strength of 16.6 kcal/mol, calculated at the B3LYP/6-311++G ÃÃ level, which is about 0.7 kcal/mol stronger than that of AA. This enhancement in the IHB strength is also consistent with the experimental results of the band frequency shifts of OH/OD and OÁ Á ÁO stretching and OH/OD out of plane bending frequencies. The theoretical calculations and spectroscopic results indicate that the IHB strength of DMHD is between those of AA and TMHD.
2013
Density functional theory (DFT) based computational study has been performed to characterize intramolecular hydrogen bonding (IMHB) interaction in a series of salicylic acid derivatives having different halogen substitution at the 5-position on the benzene ring. The molecular systems studied are salicylic acid (SA), 5-fluorosalicylic acid (5FSA), 5-chlorosalicylic acid (5ClSA) and 5-bromosalicylic acid (5BrSA). Particular emphasis has been given on the analysis of IMHB interaction by the calculation of electron density q(r) and Laplacian r 2 q(r) at the bond critical point using Atoms-In-Molecule (AIM) theory. Topological features and energy densities based on q(r) through the perturbation of the IMHB distances suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of a covalent interaction. Concomitantly, the role of charge transfer interaction in the IMHB has been critically addressed under the provision of Natural Bond Orbital (NBO) analysis. The formation of Resonance Assisted Hydrogen Bond (RAHB) in the studied molecular systems is also delineated from quantum chemical calculations. The interplay between aromaticity and RAHB is discussed in this context using both geometrical and magnetic criteria as the aromaticity descriptors. The optimized geometry features, analysis of the molecular electrostatic potential map have also been found to produce a consensus view in relation with the formation of RAHB in the studied systems. The lack of a specific pattern of IMHB energy in the studied molecules with the electronegativity of the substituent has also been attempted to address critically. Another major aspect of the present study is the argument about the superiority of quantum chemical criteria over geometrical criteria for the assessment of IMHB interaction in the studied compounds.
Tetrahedron, 2011
Three standard gas-phase B3LYP/6-31G(d) methods of the analysis of δC, δH, and JHH NMR data for solutions initially used for the title γ-lactams 1a–c led to conflicting findings on fractional populations ηs of their fast interconverting conformers A–C, which were also inconsistent with energy data. In order to find the source(s) of these discrepancies, several additional DFT computations were carried out at the double- and triple-zeta theory level with simultaneous modeling of the solutions in explicit solvents with the COSMO or IEF-PCM technique. The WC04/WP04 functionals and IGLO-II (or IGLO-III) basis set were applied for predicting δC/δH, and JHH data, respectively. The limits of efficiency and accuracy of a few current NMR-oriented computational protocols were determined by their specific use to the main forms of 1a–c treated as test cases. Thus, an unreliability of the modified Karplus-type equation for this purpose was shown. In turn, only the use of DFT-D3 corrections for the attractive van der Waals dispersion interactions (London forces) not present in conventional DFT, to Gibbs free energies (ΔG) estimated for the forms A–C of 1a–c in solution, yielded energetics and so populations (ηGs) compatible within ±15% (only ±2%, for 1a) with the best results found by considering the 1H NMR data. These ηHs were found by a linear regression of GIAO-predicted δH sets reproducing experiment in the best way (r2>0.9996, for 1a and 1b, r2=0.9970, for 1c with strongly degenerated δHs). As for ηJs, they permitted only for evaluations of the ratios (A+B)/C, excepting sufficiently differentiated JHHs (1b in acetone). In contrast, an application of δCs for assessing ηCs was unsuccessful. Selected findings were finally compared with the DP4-probability results (ηDP4s) and fairly good agreement was found. The greatest divergence in ηs exists for the C
Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding
Molecules, 2016
A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra-and inter-molecular hydrogen bonds in amides is discussed.
Magnetic Resonance in Chemistry, 2018
A comprehensive investigation was performed on 1 H, 13 C, and 31 P NMR chemical shifts (CSs) of phosphoryl benzamide derivatives (C 6 H 5 C(O)NHP(O)R 1 R 2), [R 1 , R 2 = aziridine (L 1), azetidine (L 2), pyrrolidine (L 3), piperidine (L 4), azepane (L 5), 4-methylpiperidine (L 6), propane-2-amine (L 7) and 2-methylpropane-2-amine (L 8)] by the GIAO method to find the most accordant level of theory with the experimental values. To achieve this goal, all the structures were optimized using B3LYP, BP86, PBE1PBE, M06-2X, MPWB1K and MP2 methods with 6-31+G* basis set. Computed structural parameters demonstrate that BP86 has the best agreement to the experimental values between the other methods. The def2-TZVP and aug-cc-pVDZ basis sets were also employed to inspect the effect of different types of basis sets with higher polarization and diffuse functions. The correlation between the empirical and computational values attest that 6-31+G* basis set is the optimum case regarding minimization of the costs and results. The comparison between calculated and experimental CSs at all mentioned combinations illustrated that in accordance with structural results, the best level of theory in CSs is also BP86/6-31+G*. Besides, 2 J PH values were computed with an acceptable agreement to experimental data at the optimum level of theory. The dependency between 2 J PH and the bonding structure of studied ligands was also scrutinized by the NBO analysis that interprets the relationship between the electronic properties and 2 J PH values.
Polycyclic Aromatic Compounds, 2022
Structure and stability of an inclusion complex formed by Benzocaine (BZC) and β-cyclodextrin (β-CD) were investigated computationally using different levels of theory. The conformational research based on PM6 method allowed reach two minimum-energy structures: model A and model B. The lowest conformers have been exposed to fully geometry optimization employing four DFT functionals: B3LYP, CAM-B3LYP, M05-2X and M06-2X. The performed DFT calculations have identified the model B, in which the amino group is located at the primary face of β-CD, as the most stable complex by an amount up to −40 kcal/mol. Further, the greater stabilization of model B in respect to model A, has been ascertained through AIM and NBO analyses which clarified the main hydrogen bonds HBs interactions governing the reactivity of BZC inside the hydrophobic cavity of β-CD. Finally, the estimated isotropic 1 H nuclear magnetic shielding constants generated from the gauge-including-atomic-orbital calculation have been analyzed and then compared with the available experimental data.
4_delange_et_al_2017_Struct_Chem.pdf
We have discovered, using developed by us recently FALDI and FAMSEC computational techniques, fundamentally distinct mechanisms of intramolecular red-and blue-shifted H-bond formation that occurred in different conformers of the same molecule (amino-acid β-alanine) involving the same heteroatoms (O-H⋅⋅⋅N and N-H⋅⋅⋅O). Quantitative topological, geometric and energetic data of both H-bonds obtained with well-known QTAIM and IQA methodologies agree with what is known regarding H-bonding in general. However, the FALDI charge and decomposition scheme for calculating in real space 3D conformational deformation densities provided clear evidence that the process of electron density redistribution taking place on the formation of the stronger red-shifted H-bond is fundamentally distinct from the weaker blue-shifted H-bond. Contributions made by atoms of the X-H⋅⋅⋅Y-Z fragment (IUPAC notation) as well as distinct atoms on the H-bond formation were fully explored. The FAMSEC energy decomposition approach showed that the atoms involved in formation of the red-shifted H-bond interact in a fundamentally different fashion, both locally and with the remainder of the molecule, as compared with those of the blue-shifted H-bond. Excellent correlations of trends obtained with QTAIM, IQA, FAMSEC and FALDI techniques were obtained. Commentary regarding IUPAC recommended definition of an H-bond and validity of observed AILs (or bond paths) of the two H-bond kinds is also discussed.
O NMR and DFT study of hydrogen bonding: Proton sharing and incipient transfer
Lithuanian Journal of Physics
O NMR spectra of pyridine N-oxide (PyO) complexes with the acids – acetic (AA), cyanoacetic (CyA), propiolic (PA), trichloroacetic (TCA), trifluoroacetic (TFA), hydrochloric (HCl) and methanesulfonic (MSA) – as well as some related molecules with intramolecular H-bonds (4-substituted picolinic acid N-oxides) were studied in an acetonitrile (ACN) solution. In order to evaluate the effect of proton positioning along the O–H…O bond on the measured chemical shifts the full geometry optimization was carried out, and 17O magnetic shielding tensors were calculated using density functional theory (DFT). The modified hybrid functional PBE1PBE with the 6-311++G** basis set and the gauge-including atomic orbital (GIAO) approach were applied. The solvent effect was taken into account by a polarized continuum model using the integral equation formalism (IEFPCM). Two stable structures were deduced for the PyO complexes with TCA and TFA that correspond to the H-bonds with and without proton transf...
The Journal of Organic Chemistry
NMR chemical shifts have been experimentally measured and theoretically estimated for all the carbon atoms of (1R,3S,4S,8S)-p-menthane-3,9-diol in chloroform solution. Theoretical estimations were performed using a combination of molecular dynamics simulations and quantum mechanical calculations. Molecular dynamics simulations were used to obtain the most populated conformations of the (1R,3S:4S,8S)-p-menthane-3,9-diol as well as the distribution of the solvent molecules around it. Quantum mechanical calculations of NMR chemical shifts were performed on the most relevant conformations employing the GIAO-DFT formalism. A special emphasis was put in evaluating the effects of the surrounding solvent molecules. For this purpose, supermolecule calculations were performed on complexes constituted by the solute and n chloroform molecules, where n ranges from 3 to 16. An excellent agreement with experimental data has been obtained following this computational strategy.