Spectroscopic and computational insight into weak noncovalent interactions in crystalline pyrimidine

Wright, Ashley M.; Joe, Lynn V.; Howard, Austin A.; Tschumper, Gregory S.; Hammer, Nathan I.

doi:10.1016/j.cplett.2010.11.046

Cited by 23 publications

(17 citation statements)

References 23 publications

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“…[32,[34][35][36][37][38] Solutions only contained Pm and the corresponding haloaromatic donors. Resolution of these instruments is much less than 1cm À1 and their use allows for the detection of small vibrational energy shifts due to noncovalent interactions.…”

Section: Experimental Section Raman Spectroscopymentioning

confidence: 99%

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Quantifying the Effects of Halogen Bonding by Haloaromatic Donors on the Acceptor Pyrimidine

et al. 2017

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The effects of intermolecular interactions by a series of haloaromatic halogen bond donors on the normal modes and chemical shifts of the acceptor pyrimidine are investigated by Raman and NMR spectroscopies and electronic structure computations. Halogen-bond interactions with pyrimidine's nitrogen atoms shift normal modes to higher energy and upfield shift H and C NMR peaks in adjacent nuclei. This perturbation of vibrational normal modes is reminiscent of the effects of hydrogen bonded networks of water, methanol, or silver on pyrimidine. The unexpected observation of vibrational red shifts and downfield C NMR shifts in some complexes suggests that other intermolecular forces such as π interactions are competing with halogen bonding. Natural bond orbital analyses indicate a wide range of charge transfer is possible from pyrimidine to different haloaromatic donors and computed halogen bond binding energies can be larger than a typical hydrogen bond. These results emphasize the importance in strategic selection of substituents and electron withdrawing groups in developing supramolecular structures based on halogen bonding.

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Section: Experimental Section Raman Spectroscopymentioning

confidence: 99%

“…Resolution of these instruments is much less than 1cm À1 and their use allows for the detection of small vibrational energy shifts due to noncovalent interactions. [32,[34][35][36][37][38] Solutions only contained Pm and the corresponding haloaromatic donors.…”

Section: Experimental Section Raman Spectroscopymentioning

confidence: 99%

Quantifying the Effects of Halogen Bonding by Haloaromatic Donors on the Acceptor Pyrimidine

et al. 2017

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“…Our research groups have studied the Raman vibrational spectra and the effects that noncovalent interactions and charge delocalization have on the normal modes of pyrimidine for over a decade [21,[42][43][44][45][46][47][48][49]. We have quantified hydrogen bonding interactions involving pyrimidine with water, methanol, ethylene glycol, and other species [42,43,45]; argyrophilic interactions with silver island films [48]; solid-state interactions between pyrimidine molecules [44]; and halogen bonding interactions with a variety of donors [21]. We have also demonstrated that the Raman spectra of pyrimidine in the solid-state is only weakly perturbed from that of the liquid, and that computational chemistry could be utilized to accurately assign normal modes and assess the effects of weak interactions in the solid-state [44].…”

Section: Introductionmentioning

confidence: 99%

“…We have quantified hydrogen bonding interactions involving pyrimidine with water, methanol, ethylene glycol, and other species [42,43,45]; argyrophilic interactions with silver island films [48]; solid-state interactions between pyrimidine molecules [44]; and halogen bonding interactions with a variety of donors [21]. We have also demonstrated that the Raman spectra of pyrimidine in the solid-state is only weakly perturbed from that of the liquid, and that computational chemistry could be utilized to accurately assign normal modes and assess the effects of weak interactions in the solid-state [44]. Interestingly, weak C-H•••N interactions were found to dominate the solid-state structure of pure pyrimidine and the normal modes most affected involved the displacement of hydrogen atoms.…”

Section: Introductionmentioning

confidence: 99%

A Raman Spectroscopic and Computational Study of New Aromatic Pyrimidine-Based Halogen Bond Acceptors

et al. 2019

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Two new aromatic pyrimidine-based derivatives designed specifically for halogen bond directed self-assembly are investigated through a combination of high-resolution Raman spectroscopy, X-ray crystallography, and computational quantum chemistry. The vibrational frequencies of these new molecular building blocks, pyrimidine capped with furan (PrmF) and thiophene (PrmT), are compared to those previously assigned for pyrimidine (Prm). The modifications affect only a select few of the normal modes of Prm, most noticeably its signature ring breathing mode, ν1. Structural analyses afforded by X-ray crystallography, and computed interaction energies from density functional theory computations indicate that, although weak hydrogen bonding (C–H···O or C–H···N interactions) is present in these pyrimidine-based solid-state co-crystals, halogen bonding and π-stacking interactions play more dominant roles in driving their molecular-assembly.

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“…34 Several works concerning the vibrational spectra have been conducted. 35,36 To our knowledge, less attention has been focused on pyrimidine under high pressure compared with other six-membered aromatic rings. High-pressure Raman spectra are available in the very limited range 0-0.3 GPa, which implies pyrimidine freezes at 0.2 GPa at room temperature.…”

Section: Introductionmentioning

confidence: 99%

Effect of pressure on heterocyclic compounds: Pyrimidine and s-triazine

Xiong

et al. 2014

The Journal of Chemical Physics

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We have examined the high-pressure behaviors of six-membered heterocyclic compounds of pyrimidine and s-triazine up to 26 and 26.5 GPa, respectively. Pyrimidine crystallizes in Pna2₁ symmetry (phase I) with the freezing pressure of 0.3 GPa, and transforms to another phase (phase II) at 1.1 GPa. Raman spectra of several compression-decompression cycles demonstrate there is a critical pressure of 15.5 GPa for pyrimidine. Pyrimidine returns back to its original liquid state as long as the highest pressure is below 15.1 GPa. Rupture of the aromatic ring is observed once pressure exceeds 15.5 GPa during a compression-decompression cycle, evidenced by the amorphous characteristics of the recovered sample. As for s-triazine, the phase transition from R-3c to C2/c is well reproduced at 0.6 GPa, in comparison with previous Raman data. Detailed Raman scattering experiments corroborate the critical pressure for s-triazine may locate at 14.5 GPa. That is, the compression is reversible below 14.3 GPa, whereas chemical reaction with ring opening is detected when the final pressure is above 14.5 GPa. During compression, the complete amorphization pressure for pyrimidine and s-triazine is identified as 22.4 and 15.2 GPa, respectively, based on disappearance of Raman lattice modes. Synchrotron X-ray diffraction patterns and Fourier transform infrared spectra of recovered samples indicate the products in two cases comprise of extended nitrogen-rich amorphous hydrogenated carbon (a-C:H:N).

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Spectroscopic and computational insight into weak noncovalent interactions in crystalline pyrimidine

Cited by 23 publications

References 23 publications

Quantifying the Effects of Halogen Bonding by Haloaromatic Donors on the Acceptor Pyrimidine

Quantifying the Effects of Halogen Bonding by Haloaromatic Donors on the Acceptor Pyrimidine

A Raman Spectroscopic and Computational Study of New Aromatic Pyrimidine-Based Halogen Bond Acceptors

Effect of pressure on heterocyclic compounds: Pyrimidine and s-triazine

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