scholarly journals Tetrel Bonds between Phenyltrifluorosilane and Dimethyl Sulfoxide: Influence of Basis Sets, Substitution and Competition

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7231
Author(s):  
Xiulin An ◽  
Xin Yang ◽  
Qingzhong Li
Keyword(s):  
Lone Pair ◽  
Basis Sets ◽  
Interaction Energies ◽  
Orbital Interactions ◽  
Topological Parameters ◽  
Tetrel Bond ◽  
Electron Withdrawing Group ◽  
Derivatives Of ◽  
Tetrel Bonds ◽  
Hole Interaction

Ab initio calculations have been performed for the complexes of DMSO and phenyltrifluorosilane (PTS) and its derivatives with a substituent of NH3, OCH3, CH3, OH, F, CHO, CN, NO2, and SO3H. It is necessary to use sufficiently flexible basis sets, such as aug’-cc-pVTZ, to get reliable results for the Si···O tetrel bonds. The tetrel bond in these complexes has been characterized in views of geometries, interaction energies, orbital interactions and topological parameters. The electron-donating group in PTS weakens this interaction and the electron-withdrawing group prominently strengthens it to the point where it exceeds that of the majority of hydrogen bonds. The largest interaction energy occurs in the p-HO3S-PhSiF3···DMSO complex, amounting to −122 kJ/mol. The strong Si···O tetrel bond depends to a large extent on the charge transfer from the O lone pair into the empty p orbital of Si, although it has a dominant electrostatic character. For the PTS derivatives of NH2, OH, CHO and NO2, the hydrogen bonded complex is favorable to the tetrel bonded complex for the NH2 and OH derivatives, while the σ-hole interaction prefers the π-hole interaction for the CHO and NO2 derivatives.

Characterizing the lone pair⋯π–hole interaction in complexes of ammonia with perfluorinated arenes

2021 ◽  
Vol 23 (15) ◽  
pp. 9121-9129
Author(s):  
Weixing Li ◽  
Imanol Usabiaga ◽  
Camilla Calabrese ◽  
Luca Evangelisti ◽  
Assimo Maris ◽  
...  
Keyword(s):  
Lone Pair ◽  
Hole Interaction

Stronger and more flexible lone pair⋯π–hole interaction of ammonia with respect to water in complexes with perfluorinated arenes.

The assessment of density functionals for DNA–protein stacked and T-shaped complexes

2010 ◽  
Vol 88 (8) ◽  
pp. 815-830 ◽  
Author(s):  
Lesley R. Rutledge ◽  
Stacey D. Wetmore
Keyword(s):  
Amino Acid ◽  
Potential Energy ◽  
Large Scale ◽  
Enzymatic Reaction ◽  
Basis Sets ◽  
Density Functionals ◽  
Interaction Energies ◽  
Π Interactions ◽  
Hybrid Techniques ◽  
Semi Empirical

The present work uses 129 nucleobase – amino acid CCSD(T)/CBS stacking and T-shaped interaction energies as reference data to test the ability of various density functionals with double-zeta quality basis sets, as well as some semi-empirical and molecular mechanics methods, to accurately describe noncovalent DNA–protein π–π and π+–π interactions. The goal of this work is to identify methods that can be used in hybrid approaches (QM/MM, ONIOM) for large-scale modeling of enzymatic systems involving active-site (substrate) π–π contacts. Our results indicate that AMBER is a more appropriate choice for the lower-level method in hybrid techniques than popular semi-empirical methods (AM1, PM3), and suggest that AMBER accurately describes the π–π interactions found throughout DNA–protein complexes. The M06–2X and PBE-D density functionals were found to provide very promising descriptions of the 129 nucleobase – amino acid interaction energies, which suggests that these may be the most suitable methods for describing high-level regions. Therefore, M06–2X and PBE-D with both the 6–31G(d) and 6–31+G(d,p) basis sets were further examined through potential-energy surface scans to better understand how these techniques describe DNA–protein π–π interactions in both minimum and nonminimum regions of the potential-energy surfaces, which is critical information when modeling enzymatic reaction pathways. Our results suggest that studies of stacked nucleobase – amino acid systems should implement the PBE-D/6–31+G(d,p) method. However, if T-shaped contacts are involved and (or) smaller basis sets must be considered due to limitations in computational resources, then M06–2X/6–31G(d) provides an overall excellent description of both nucleobase – amino acid stacking and T-shaped interactions for a range of DNA–protein π–π and π+–π interactions.

The Through-Bond Interaction of a Sulfur Lone Pair with Oxygenated Substituents in the Thiacyclohexane Framework

2005 ◽  
Vol 58 (7) ◽  
pp. 531
Author(s):  
Laura Andrau ◽  
Jonathan M. White
Keyword(s):  
Low Temperature ◽  
Crystal Structures ◽  
Bond Distance ◽  
Lone Pair ◽  
X Ray ◽  
Ester Derivative ◽  
Bond Interaction ◽  
Derivatives Of ◽  
Electron Demand

Low-temperature X-ray crystal structures were determined on a range of derivatives of 4-thiacyclohexanol 5a of varying electron demand with a view to finding evidence for a through-bond interaction between the sulfur lone pair and the oxygenated substituent. In contrast to earlier suggestions, plots of C–OR bond distance versus pKa (ROH) showed that any interaction between the sulfur and the OR group is unlikely to be of a through-bond origin. Furthermore, unimolecular solvolysis rate measurements on the nosylate ester derivative 5g showed that the sulfur actually retards the reaction slightly in comparison with the corresponding sulfur-free analogue 6.

scholarly journals Electronically Excited States of Potential Interstellar, Anionic Building Blocks for Astrobiological Nucleic Acids

2021 ◽  
Vol 8 ◽  
Author(s):  
Taylor J. Santaloci ◽  
Marie E. Strauss ◽  
Ryan C. Fortenberry
Keyword(s):  
Nucleic Acids ◽  
Excited States ◽  
Lone Pair ◽  
Building Blocks ◽  
Hydroxyl Group ◽  
Quantum Chemical Analysis ◽  
Electronically Excited States ◽  
Neutral Radical ◽  
Electronically Excited ◽  
Electron Withdrawing Group

Functionalizing deprotonated polycyclic aromatic hydrocarbon (PAH) anion derivatives gives rise to electronically excited states in the resulting anions. While functionalization with −OH and −C2H, done presently, does not result in the richness of electronically excited states as it does with −CN done previously, the presence of dipole-bound excited states and even some valence excited states are predicted in this quantum chemical analysis. Most notably, the more electron withdrawing −C2H group leads to valence excited states once the number of rings in the molecule reaches three. Dipole-bound excited states arise when the dipole moment of the corresponding neutral radical is large enough (likely around 2.0 D), and this is most pronounced when the hydrogen atom is removed from the functional group itself regardless of whether functionalized by a hydroxyl or enthynyl group. Deprotonatation of the hydroxyl group in the PAH creates a ketone with a delocalized highest occupied molecular orbital (HOMO) unlike deprotonation of a hydrogen on the ring where a localized lone pair on one of the carbon atoms serves as the HOMO. As a result, hydroxyl functionlization and subsequent deprotonation of PAHs creates molecules that begin to exhibit structures akin to nucleic acids. However, the electron withdrawing −C2H has more excited states than the electron donating −OH functionalized PAH. This implies that the −C2H electron withdrawing group can absorb a larger energy range of photons, which signifies an increasing likelihood of being stabilized in the harsh conditions of the interstellar medium.

N.M.R. spectra and stereochemistry of the bipyridyls. III. 2,2'-Bipyridyl and dimethyl derivatives, 3,3'- bipyridyl, and 4,4' - bipyridyl

1967 ◽  
Vol 20 (6) ◽  
pp. 1227 ◽  
Author(s):  
TM Spotswood ◽  
CI Tanzer
Keyword(s):  
Hydrogen Bonding ◽  
Electrostatic Field ◽  
Field Effect ◽  
Chemical Shifts ◽  
Lone Pair ◽  
Diamagnetic Anisotropy ◽  
Equal Importance ◽  
Nitrogen Lone Pair ◽  
Lone Pair Electrons ◽  
Derivatives Of

The analysis of the n.m.r, spectra of 2,2?-, 3,3?-, and 4,4?-bipyridyl and three dimethyl-2,2?-bipyridyls is reported and the factors determining the relative chemical shifts of the ring protons and methyl groups in several solvents are discussed. The diamagnetic anisotropy of the neighbouring ring and electrostatic field effect of the nitrogen lone pair electrons are shown to be of roughly equal importance for derivatives of 2,2?-bipyridyl except in hydrogen bonding solvents. Attenuation of the electrostatic field effect in polar, and particularly in hydrogen bonding solvents, is established for 4- picoline, and for the bipyridyls, and this effect is responsible for striking changes in the spectrum of 2,2?-bipyridyl in hydrogen bonding solvents. An approximate interplanar angle of 58� is derived for 3,3?- dimethyl-2,2?-bipyridyl, and 2,2?-bipyridyl and its 4,4?- and 5,5?- dimethyl derivatives appear to be trans coplanar in all solvents. 3,3?- Bipyridyl and 4,4?-bipyridyl are probably highly twisted in all solvents, or alternatively, behave as essentially free rotors. The predicted conformations are in good agreement with the electronic spectral data.

The coulombic σ-hole model describes bonding in CX3I⋯Y− complexes completely

2018 ◽  
Vol 20 (35) ◽  
pp. 22849-22855 ◽  
Author(s):  
Timothy Clark ◽  
Andreas Heßelmann
Keyword(s):  
Interaction Energies ◽  
Halide Anions ◽  
Hole Model ◽  
Hole Interaction

Contrary to recent reports, the σ-hole interaction energies of complexes between the carbon tetrahalides CX3I (X = F, Cl, Br, I) and halide anions Y− (Y = F, Cl, Br, I) are described very well by the simple Coulombic σ-hole concept if it is applied properly.

Universal Gaussian basis functions in relativistic quantum chemistry: atomic Dirac–Fock–Coulomb and Dirac–Fock–Breit calculations

1992 ◽  
Vol 70 (6) ◽  
pp. 1822-1826 ◽  
Author(s):  
G. L. Malli ◽  
A. B. F. Da Silva ◽  
Yasuyuki Ishikawa
Keyword(s):  
Relativistic Quantum ◽  
Basis Set ◽  
Basis Sets ◽  
Interaction Energies ◽  
Gaussian Basis Sets ◽  
Consistent Field ◽  
Self Consistent ◽  
Self Consistent Field ◽  
Gaussian Basis Set ◽  
Good Agreement

Matrix Dirac–Fock–Coulomb and Dirac–Fock–Breit self-consistent field calculations are performed for a number of neutral atoms. He (Z = 2) through Xe (Z = 54), using the universal Gaussian basis set (18s, 12p, 11d) reported recently by Da Silva etal. The total Dirac–Fock–Coulomb, the Dirac–Fock–Breit, and the Breit interaction energies calculated with this universal Gaussian basis set are in good agreement with the corresponding values obtained by using an extensive well-tempered Gaussian basis set for the He through Ca (Z = 20) atoms. Although this universal Gaussian basis set is inadequate for the calculation of total Dirac–Fock–Coulomb and Dirac–Fock–Breit energies for the Kr, Sr, and Xe atoms, the Breit interaction energies calculated with this basis for these three atoms are in very good agreement with the corresponding Breit interaction energies obtained by using the extensive well-tempered Gaussian basis sets. Work is in progress to generate a more extensive and energetically better universal Gaussian basis set for He through Xe for its use in non-relativistic Hartree–Fock as well as Dirac–Fock self-consistent field calculations on polyatomics involving heavy atoms.

Computational electrochemistry study of derivatives of anthraquinone and phenanthraquinone analogues: the substitution effect

RSC Advances ◽  
2016 ◽  
Vol 6 (92) ◽  
pp. 89827-89835 ◽  
Author(s):  
Zhen Wang ◽  
Anyang Li ◽  
Lei Gou ◽  
Jingzheng Ren ◽  
Gaohong Zhai
Keyword(s):  
Redox Potential ◽  
Functional Group ◽  
Substitution Effect ◽  
Single Electron ◽  
Group Position ◽  
Computational Electrochemistry ◽  
Electron Withdrawing Group ◽  
Derivatives Of

Effects of functional group position on the calculated redox potential for the single electron-withdrawing group substitution of phenanthraquinone analogues.

scholarly journals Toward a uniform description of hydrogen bonds and halogen bonds: correlations of interaction energies with various geometric, electronic and topological parameters

RSC Advances ◽  
2017 ◽  
Vol 7 (17) ◽  
pp. 10295-10305 ◽  
Author(s):  
Jian-Wei Zou ◽  
Meilan Huang ◽  
Gui-Xiang Hu ◽  
Yong-Jun Jiang
Keyword(s):  
Hydrogen Bonds ◽  
Structural Parameters ◽  
Interaction Energies ◽  
Halogen Bonds ◽  
Topological Parameters

Correlations between interaction energies and various structural parameters were established to reveal the differences between hydrogen bonds and halogen bonds.

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