Characterizing Hydrogen Bonding in Uracil–Nitrosamine Complexes through One- and Two-Bond Spin–Spin Coupling Constants across Hydrogen Bonds

Roohi, Hossein; Anjomshoa, Elham

doi:10.1246/bcsj.20100350

Cited by 3 publications

(2 citation statements)

References 29 publications

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“…This value is calculated through the GIAO absolute shielding constant. The NMR shielding at ring centres (the non-weighted mean of the heavy atom coordinates) is a NICS (0); and 1.0 Å above the ring centre is a NICS (1) [47]. Here, the shift was interpreted for all parameters through the relation A = A (complex)-A (monomer).…”

Section: Methodsmentioning

confidence: 99%

A theoretical perspective of the nature of hydrogen-bond types – the atoms in molecules approach

2013

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Hydrogen bonds and their strength were analysed based on their X-H proton-donor bond properties and the parameters of the H-Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and NICS (0), NICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.

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Section: Methodsmentioning

confidence: 99%

A theoretical perspective of the nature of hydrogen-bond types – the atoms in molecules approach

2013

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“…The NMR shielding at ring centers (the non-weighted mean of heavy-atom coordinates) is a NICS (0); a NICS (1) is 1.0 Å above the ring center. 27 Bader's theory of atoms in molecules (AIM) was employed to find the critical points and to analyze the electron densities and their Laplacians. The properties of bond critical points (BCPs) were studied, including electron density (r), its Laplacian (D 2 r) and the ellipticity at a BCP.…”

Section: Computational Detailsmentioning

confidence: 99%

Do resonance-assisted intramolecular halogen bonds exist without a charge transfer and a σ-hole?

Pandiyan

Deepa

Kolandaivel

2015

Phys. Chem. Chem. Phys.

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To analyze the properties and mechanisms of six types of intramolecular resonance-assisted halogen bonds (Br···O, Cl···O, F···O, Br···O, Cl···S and F···S), we have chosen the five-membered closed ring system X-C1R1=C3R2-C2R3=Y (X = Br, Cl & F; Y = O & S) of unsaturated compounds with the substituents NO2, CH3 and H. A total of 78 structures were investigated by quantum chemical calculations at the MP2/aug-cc-pVTZ level of theory. A molecular electrostatic potential (MESP) map reveals that the cusp point of the σ-hole was not utilized but the belt point was used for all these intramolecular halogen-bonding interactions, indicating that all are electrostatic interactions. The halogen-bonding angle is below 100° with the strongest interactions. The value of the nucleus-independent chemical shift (NICS (1)) reflects the changes and efficiency of resonance in all structures with a long bond. The presence of all interactions was proved by the bond critical point (BCP) and analyzed through its electron density, Laplacian of electron density and ellipticity parameter. The linear-probability correlation between the difference of the sum of the van der Waals radius and the non-covalent bond length (∑vdW-L) and the electron density of the BCP was reported. 2D and 3D-NCI (non covalent interactions) plots show that halogen-bonding interactions are a mixed type of interactions with an attractive term. Natural bond orbital (NBO) analysis clearly indicates that the halogen bond lacks charge transfer and orbital overlapping through non-interacting lobes.

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How do halogen bonds (S–O⋯I, N–O⋯I and C–O⋯I) and halogen–halogen contacts (C–I⋯I–C, C–F⋯F–C) subsist in crystal structures? A quantum chemical insight

2016

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Thirteen X-ray crystal structures containing various non-covalent interactions such as halogen bonds, halogen-halogen contacts and hydrogen bonds (I⋯N, I⋯F, I⋯I, F⋯F, I⋯H and F⋯H) were considered and investigated using the DFT-D3 method (B97D/def2-QZVP). The interaction energies were calculated at MO62X/def2-QZVP and MP2/aug-cc-pvDZ level of theories. The higher interaction and dispersion energies (2nd crystal) of -9.58 kcal mol and -7.10 kcal mol observed for 1,4-di-iodotetrafluorobenzene bis [bis (2-phenylethyl) sulfoxide] structure indicates the most stable geometrical arrangement in the crystal packing. The electrostatic potential values calculated for all crystal structures have a positive σ-hole, which aids understanding of the nature of σ-hole bonds. The significance of the existence of halogen bonds in crystal packing environments was authenticated by replacing iodine atoms by bromine and chlorine atoms. Nucleus independent chemical shift analysis reported on the resonance contribution to the interaction energies of halogen bonds and halogen-halogen contacts. Hirshfeld surface analysis and topological analysis (atoms in molecules) were carried out to analyze the occurrence and strength of all non-covalent interactions. These analyses revealed that halogen bond interactions were more dominant than hydrogen bonding interactions in these crystal structures. Graphical Abstract Molecluar structure of 1,4-Di-iodotetrafluorobenzene bis(thianthrene 5-oxide) moelcule and its corresponding molecular electrostatic potential map for the view of σ-hole.

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Characterizing Hydrogen Bonding in Uracil–Nitrosamine Complexes through One- and Two-Bond Spin–Spin Coupling Constants across Hydrogen Bonds

Cited by 3 publications

References 29 publications

A theoretical perspective of the nature of hydrogen-bond types – the atoms in molecules approach

A theoretical perspective of the nature of hydrogen-bond types – the atoms in molecules approach

Do resonance-assisted intramolecular halogen bonds exist without a charge transfer and a σ-hole?

How do halogen bonds (S–O⋯I, N–O⋯I and C–O⋯I) and halogen–halogen contacts (C–I⋯I–C, C–F⋯F–C) subsist in crystal structures? A quantum chemical insight

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