A QTAIM exploration of the competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems

Huan, Guo; Xu, Ting; Momen, Roya; Wang, Lingling; Yang, Ping; Kirk, Steven R.; Jenkins, Samantha; Mourik, Tanja van

doi:10.1016/j.cplett.2016.09.031

Cited by 10 publications

(7 citation statements)

References 38 publications

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“…[29,30] By combining interactions that do not compete for the same binding sites, it is, in principle, possible to avoid or at least minimize ''synthon cross-over'', [31] thereby producing architectures of considerable complexity. [34][35][36][37][38][39][40][41][42][43] This is not only because HBs and XBs are similar in strength and properties, but also they are widely applicable to biochemistry and drug design. [33] There are many studies on the competition between various interactions, especially the competition between hydrogen and halogen bonds.…”

Section: Introductionmentioning

confidence: 99%

“…[33] There are many studies on the competition between various interactions, especially the competition between hydrogen and halogen bonds. [34][35][36][37][38][39][40][41][42][43] This is not only because HBs and XBs are similar in strength and properties, but also they are widely applicable to biochemistry and drug design. Alkorta et al studied HBs and XBs formed between hypohalous acid and three nitrogen-containing bases .…”

Section: Introductionmentioning

confidence: 99%

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Tuning the Competition between Hydrogen and Tetrel Bonds by a Magnesium Bond

2020

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A computational study of the complexes formed by TF 3 OH (T=C, Si, Ge) with three nitrogen-containing bases NCH, NH 3 , and imidazole (IM) is carried out at the MP2/aug-cc-pVTZ level. TF 3 OH can participate in two different types of noncovalent interactions: a hydrogen bond (HB) involving the hydroxyl proton and a tetrel bond (TB) with the tetel atom T. The strength of the HB is largely unaffected by the identity of T while the TB is enhanced as T grows larger. The HB is preferred over the TB for most systems, with the exception of GeF 3 OH with either NH 3 or IM. MgCl 2 engages in a Mg···O Magnesium bond (Mg-bond) with the TF 3 OH O atom, which cooperatively enhances both the HB and TB. The HB strengthening is particularly large for the NH 3 or IM bases, and especially for CF 3 OH, but is slowly reduced as the T atom grows larger. The TB enhancement, on the other hand, behaves in the opposite fashion, accelerating for the larger T atoms. As a bottom line, the Mg-bond generally reinforces and accentuates the preference for the HB or TB that is already present in the dimer. The Mg-bond is also responsible for a proton transfer in the HB configurations with NH 3 and IM.[a] Dr.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Tuning the Competition between Hydrogen and Tetrel Bonds by a Magnesium Bond

2020

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“…Following their footsteps on the path they traced, we here present the experimental charge density analysis of 1-methyluracil (hereinafter 1-MUR), based on a very low-T dataset collected at Caltech in Marsh’s laboratory in 1989 by one of us (RD). Experimental as well as theoretical and computational work on 1-methyluracil and its derivatives have been published a number of times [ 2 , 3 , 4 , 5 , 6 , 7 ], yet the experimental estimates for some of the fundamental properties of the molecule in a condensed phase, such as integrated atomic volumes and charges, as well as atomic and molecular electrostatic quadrupole moments, are not available, to the best of our knowledge, in the literature.…”

Section: Introductionmentioning

confidence: 99%

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

et al. 2021

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The experimental electron density distribution (EDD) of 1-methyluracil (1-MUR) was obtained by single crystal X-ray diffraction (XRD) experiments at 23 K. Four different structural models fitting an extensive set of XRD data to a resolution of (sinθ/λ)max = 1.143 Å−1 are compared. Two of the models include anharmonic temperature factors, whose inclusion is supported by the Hamilton test at a 99.95% level of confidence. Positive Fourier residuals up to 0.5 eÅ–3 in magnitude were found close to the methyl group and in the region of hydrogen bonds. Residual density analysis (RDA) and molecular dynamics simulations in the solid-state demonstrate that these residuals can be likely attributed to unresolved disorder, possibly dynamical and long–range in nature. Atomic volumes and charges, molecular moments up to hexadecapoles, as well as maps of the molecular electrostatic potential were obtained from distributed multipole analysis of the EDD. The derived electrostatic properties neither depend on the details of the multipole model, nor are significantly affected by the explicit inclusion of anharmonicity in the least–squares model. The distribution of atomic charges in 1-MUR is not affected by the crystal environment in a significant way. The quality of experimental findings is discussed in light of in-crystal and gas-phase quantum simulations.

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“…The authors investigated the (Y = Br, I, At)/halogenabenzene/NH 3 system [3] and concluded that a halogen bond and a hydrogen bond form with the NH 3 nucleophile. We previously observed for the (X = F, Cl, Br, I, At)/1-methyluracil/H 2 O system that the strength of the hydrogen bond decreased with increasing halogen size, and the hydrogen bonds displayed an admixture of covalent character, but all the halogen bonds were purely electrostatic in nature [5].…”

Section: Introductionmentioning

confidence: 99%

Halogen and Hydrogen Bonding in Halogenabenzene/NH3 Complexes Compared Using Next-Generation QTAIM

Mourik

et al. 2019

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Next-generation quantum theory of atoms in molecules (QTAIM) was used to investigate the competition between hydrogen bonding and halogen bonding for the recently proposed (Y = Br, I, At)/halogenabenzene/NH3 complex. Differences between using the SR-ZORA Hamiltonian and effective core potentials (ECPs) to account for relativistic effects with increased atomic mass demonstrated that next-generation QTAIM is a much more responsive tool than conventional QTAIM. Subtle details of the competition between halogen bonding and hydrogen bonding were observed, indicating a mixed chemical character shown in the 3-D paths constructed from the bond-path framework set B. In addition, the use of SR-ZORA reduced or entirely removed spurious features of B on the site of the halogen atoms.

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A QTAIM exploration of the competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems

Cited by 10 publications

References 38 publications

Tuning the Competition between Hydrogen and Tetrel Bonds by a Magnesium Bond

Tuning the Competition between Hydrogen and Tetrel Bonds by a Magnesium Bond

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

Halogen and Hydrogen Bonding in Halogenabenzene/NH3 Complexes Compared Using Next-Generation QTAIM

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