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<p>In this study, a urea clathrate (UC) crystal structure was successfully grown and analyzed using single-crystal–X-ray diffraction (SC − XRD) and computational methods. After a slow evaporation period of 20&#xa0;days, the crystal adopts a tetrahedral geometry within the P − 42<sub>1</sub>&#xa0;m space group. Their Hirshfeld surface analysis reveals that their O<i> − </i>H (~ 31.3%) and C<i> − </i>H (~ 29.3%) interactions may be the key players in stabilizing its geometry. Crystallographic Information File (CIF) is used as an input file for computational approaches to investigate its theoretical interactions with tobacco alkaloids. Its density of states (DOS) by its optimized geometries shows that it maintains a distance ~ 2.82 − 3.16&#xa0;Å from these alkaloids while it also demonstrates an excellent recovery time of ~ 2.89 × 10<sup>−19</sup>&#xa0;s. Their molecular charges have suggested that the charge mostly concentrates over the alkaloids. Its Natural Bond Orbital (NBO) analysis highlights key transitions, notably the strong hyperconjugation between (C1 − C2)π → (C1 − C7) π* (1.15&#xa0;kcal/mol) and (N4)π → (C1 − C2)π* (5.93&#xa0;kcal/mol), influencing its electronic structure and reactivity.</p>

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Experimental and Theoretical Studies on a New Urea Clathrate Crystal: X-ray Diffraction, Hirshfeld Surface Analysis, RDG − NCI, FMOs, and NBO Analysis

  • 期刊论文

  • 发表日期：

    2025年4月3日

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  • Wardha Zafar,
  • Sadaf Noreen,
  • Ashraf Y. Elnaggar,
  • Mohamed H. H. Mahmoud,
  • Islam H. El Azab

摘要

In this study, a urea clathrate (UC) crystal structure was successfully grown and analyzed using single-crystal–X-ray diffraction (SC − XRD) and computational methods. After a slow evaporation period of 20 days, the crystal adopts a tetrahedral geometry within the P − 421 m space group. Their Hirshfeld surface analysis reveals that their O − H (~ 31.3%) and C − H (~ 29.3%) interactions may be the key players in stabilizing its geometry. Crystallographic Information File (CIF) is used as an input file for computational approaches to investigate its theoretical interactions with tobacco alkaloids. Its density of states (DOS) by its optimized geometries shows that it maintains a distance ~ 2.82 − 3.16 Å from these alkaloids while it also demonstrates an excellent recovery time of ~ 2.89 × 10−19 s. Their molecular charges have suggested that the charge mostly concentrates over the alkaloids. Its Natural Bond Orbital (NBO) analysis highlights key transitions, notably the strong hyperconjugation between (C1 − C2)π → (C1 − C7) π* (1.15 kcal/mol) and (N4)π → (C1 − C2)π* (5.93 kcal/mol), influencing its electronic structure and reactivity.