Quantitative Evaluation of C–H···O and C–H···π Intermolecular Interactions in Ethyl-3-benzyl-1-methyl-2-oxoindoline-3-carboxylate and 3-Methyl-but-2-en-1-yl-1,3-dimethyl-2-oxoindoline-3-carboxylate: Insights from PIXEL and Hirshfeld Analysis (original) (raw)
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Journal of Chemical Theory and Computation, 2010
The strengths of noncovalent interactions are generally very sensitive to a number of geometric parameters. Among the most important of these parameters is the separation between the interacting moieties (in the case of an intermolecular interaction, this would be the intermolecular separation). Most works seeking to characterize the properties of intermolecular interactions are mainly concerned with binding energies obtained at the potential energy minimum (as determined at some particular level of theory). In this work, in order to extend our understanding of these types of noncovalent interactions, we investigate the distance dependence of several types of intermolecular interactions, these are hydrogen bonds, stacking interactions, dispersion interactions, and X-H · · · π interactions. There are several methods that have traditionally been used to treat noncovalent interactions as well as many new methods that have emerged within the past three or four years. Here we obtain reference data using estimated CCSD(T) values at the complete basis set limit (using the CBS(T) method); potential energy curves are also produced using several other methods thought to be accurate for intermolecular interactions, these are MP2/cc-pVTZ, MP2/aug-cc-pVDZ, MP2/6-31G*(0.25), SCS(MI)-MP2/cc-pVTZ, estimated MP2.5/CBS, DFT-SAPT/ aug-cc-pVTZ, DFT/M06-2X/6-311+G(2df,2p), and DFT-D/TPSS/6-311++G(3df,3pd). The basis set superposition error is systematically considered throughout the study. It is found that the MP2.5 and DFT-SAPT methods, which are both quite computationally intensive, produce potential energy curves that are in very good agreement to those of the reference method. Among the MP2 techniques, which can be said to be of medium computational expense, the best results are obtained with MP2/cc-pVTZ and SCS(MI)-MP2/cc-pVTZ. DFT-D/TPSS/6-311++G(3df,3pd) is the DFT-based method that can be said to give the most well-balanced description of intermolecular interactions.
International Journal of Molecular Sciences, 2022
N-(4-((3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)selanyl)phenyl)acetamide (5), C19H15NO3Se, was prepared in two steps from 4,4′-diselanediyldianiline (3) via reduction and subsequent nucleophilic reaction with 2-methyl-3-bromo-1,4-naphthalenedione, followed by acetylation with acetic anhydride. The cytotoxicity was estimated against 158N and 158JP oligodendrocytes and the redox profile was also evaluated using different in vitro assays. The technique of single-crystal X-ray diffraction is used to confirm the structure of compound 5. The enantiopure 5 crystallizes in space group P21 with Flack parameter 0.017 (8), exhibiting a chiral layered absolute structure. Molecular structural studies showed that the crystal structure is foremost stabilized by N-H···O and relatively weak C-H···O contacts between molecules, and additionally stabilized by weak C-H···π and Se···N interactions. Hirshfeld surface analysis is used to quantitatively investigate the noncovalent interactions that sta...
Journal of Molecular Modeling, 2021
The compound 1,3,3-trimethyl-2-oxabicyclo[2.2.2]octan-9-ol (9-hydroxyeucaliptol) has been prepared and characterized by single-crystal X-ray diffraction analysis, infrared, Raman, and UV-visible spectroscopies. The molecular geometry of the title compound was also investigated theoretically by density functional theory (DFT) calculations to compare with the experimental data. The substance crystallizes in the trigonal crystal system, space group P3 2 with Z = 9 molecules per unit cell. There are three independent molecules in the crystal asymmetric unit having the same chirality and showing some differences in the orientation of the H-atom of the hydroxyl group. The crystal structure of 9-hydroxyeucaliptol shows that the hydroxyl group presents an anticonformation with respect to the O-atom of the ether group. The crystal packing of 9-hydroxyeucaliptol is stabilized by intermolecular O-H•••O hydrogen bonds involving the hydroxyl groups of different molecules, which play a decisive role in the preferred conformation adopted in solid state. The intermolecular interactions observed in solid state were also studied through the Hirshfeld surface analysis and quantum theory of atoms in molecules (QTAIM) approaches. Energy framework calculations have also been carried out to analyze and visualize the topology of the supramolecular assembly, and the results indicate a significant contribution from electrostatic energy over the dispersion.
Acta Crystallographica Section E Crystallographic Communications
The crystal structures of the disordered hemi-DMSO solvate of (E)-2-oxo-N′-(3,4,5-trimethoxybenzylidene)-2H-chromene-3-carbohydrazide, C20H18N2O6·0.5C2H6OS, and (E)-N′-benzylidene-2-oxo-2H-chromene-3-carbohydrazide, C17H12N2O3 (4: R = C6H5), are discussed. The non-hydrogen atoms in compound [4: R = (3,4,5-MeO)3C6H2)] exhibit a distinct curvature, while those in compound, (4: R = C6H5), are essential coplanar. In (4: R = C6H5), C—H...O and π–π intramolecular interactions combine to form a three-dimensional array. A three-dimensional array is also found for the hemi-DMSO solvate of [4: R = (3,4,5-MeO)3C6H2], in which the molecules of coumarin are linked by C—H...O and C—H...π interactions, and form tubes into which the DMSO molecules are cocooned. Hirshfeld surface analyses of both compounds are reported, as are the lattice energy and intermolecular interaction energy calculations of compound (4: R = C6H5).
Journal of Physical Chemistry B, 2000
Experimental X-ray charge densities from low-temperature data are used in the evaluation of the intermolecular interactions and lattice energies of crystals of glycylglycine, DL-histidine, and DL-proline. The X-ray analysis leads to a set of atom-centered distributed multipoles, from which electrostatic interactions are calculated. Nonempirical exp-6 atom-atom potentials are used to calculate the smaller contributions of van der Waals interactions. For comparison, parallel theoretical calculations are performed on the molecular dimers (B3LYP) and the periodic crystals (Periodic Hartree-Fock, PHF). The dimer interactions show good agreement with experimental values, except for the strongest interactions in the glycylglycine crystal. The experimental charge density results correlate well with those based on the PHF calculations, but quantitative agreement for the interaction energies is only obtained after application of a scaling factor of ∼0.76 to the PHF values. The discrepancy is attributed to the well-known overestimate of molecular polarity in the HF method, resulting from neglect of electron correlation. The agreement between lattice energies derived from the experimental charge density and theoretical values from the PHF calculations is within 10 kJ/mol for the crystals examined in this study. The study provides the basis for use of experimental electrostatic moments in molecular modeling calculations of more complex systems.
2015
quantitative analysis of the intermolecular interactions in the crystal structure of a pyrazole derivative namely 4-(2-(ethoxymethyl) phenyl)- 1H-pyrazol-3-ol has been performed. The compound crystallizes with one molecule in the asymmetric unit in the monoclinic centrosymmetric space group P2 1 /n. SCXRD studies revealed the presence of O-H…N, N-H…O H-bonds along with C-H…O, C-H…π and H…H interactions in the crystal. The molecular electrostatic map clearly demonstrates the nature of different atoms within the molecule. The lattice energy of the compound was calculated using PIXEL. The decomposition of the interaction energies obtained for different molecular pairs clearly demonstrated that the nature and strength of interactions present in a given molecular pair was directly correlated with the strength of the donor or/and acceptor atom present in the molecule.
Journal of Physical Chemistry B, 2000
Experimental X-ray charge densities from low-temperature data are used in the evaluation of the intermolecular interactions and lattice energies of crystals of glycylglycine, DL-histidine, and DL-proline. The X-ray analysis leads to a set of atom-centered distributed multipoles, from which electrostatic interactions are calculated. Nonempirical exp-6 atom-atom potentials are used to calculate the smaller contributions of van der Waals interactions. For comparison, parallel theoretical calculations are performed on the molecular dimers (B3LYP) and the periodic crystals (Periodic Hartree-Fock, PHF). The dimer interactions show good agreement with experimental values, except for the strongest interactions in the glycylglycine crystal. The experimental charge density results correlate well with those based on the PHF calculations, but quantitative agreement for the interaction energies is only obtained after application of a scaling factor of ∼0.76 to the PHF values. The discrepancy is attributed to the well-known overestimate of molecular polarity in the HF method, resulting from neglect of electron correlation. The agreement between lattice energies derived from the experimental charge density and theoretical values from the PHF calculations is within 10 kJ/mol for the crystals examined in this study. The study provides the basis for use of experimental electrostatic moments in molecular modeling calculations of more complex systems.