Uracil Derivatives for Halogen-Bonded Cocrystals.
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ABSTRACT:
SUBMITTER: Benito M
PROVIDER: S-EPMC8508742 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:In this work, we explore the halogen-bonded cocrystallization potential of cobaloxime complexes in the synthesis of cocrystals with perhalogenated benzenes. We demonstrate a strategy for synthesizing halogen-bonded metal-organic cocrystals by utilizing cobaloximes whose pendant bromide group and oxime oxygen enable halogen bonding. By combining three well-known halogen bond donor molecules differing in binding geometry and composition with three cobaloxime units, we obtained a total of four previously unreported cocrystals. Single crystal X-ray diffraction experiments showed that the majority of obtained cocrystals exhibited the formation of the targeted I···O and I···Br motives. These results illustrate the potential of cobaloximes as halogen bond acceptors and indicate that this type of halogen bond acceptors may offer a novel route to metal-organic halogen-bonded cocrystals.
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Project description:The halogen-bond (X-bond) donors 1,3- and 1,4-diiodotetrafluorobenzene (1,3-di-I-tFb and 1,4-di-I-tFb, respectively) form cocrystals with trans-1,2-bis(2-pyridyl)ethylene (2,2'-bpe) assembled by N···I X-bonds. In each cocrystal, 2(1,3-di-I-tFb)·2(2,2'-bpe) and (1,4-di-I-tFb)·(2,2'-bpe), the donor molecules support the C=C bonds of 2,2'-bpe to undergo an intermolecular [2+2] photodimerization. UV irradiation of each cocrystal resulted in stereospecific and quantitative conversion of 2,2'-bpe to rctt-tetrakis(2-pyridyl)cyclobutane (2,2'-tpcb). In each case, the reactivity occurs via face-to-face ?-stacked columns wherein nearest-neighbor pairs of 2,2'-bpe molecules lie sandwiched between X-bond donor molecules. Nearest-neighbor C=C bonds are stacked criss-crossed in both cocrystals. The reactivity was ascribed to the olefins undergoing pedal-like motion in the solid state. The stereochemistry of 2,2'-tpcb is confirmed in cocrystals 2(1,3-di-I-tFb)·(2,2'-tpcb) and (1,4-di-I-tFb)·(2,2'-tpcb).
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Project description:We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of uracil and its derivatives in the gas phase and water. The values of these parameters showed that the most stable tautomer is the least aromatic. A good performance of newly designed xOPBE density functional in combination with both large aug-cc-pVQZ and small STO(1M)-3G basis sets for predicting chemical shifts of uracil and 5-fluorouracil in vacuum and water was observed. As a practical alternative for calculating the chemical shifts of challenging heterocyclic compounds, we also propose B3LYP calculations with small STO(1M)-3G basis set. The indirect spin-spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well.
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Project description:Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine-guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).
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Project description:The formation of non-covalent directional interactions, such as hydrogen or halogen bonds, is a central concept of materials design, which hinges on using small compact atoms of the 2nd period, notably nitrogen and oxygen, as acceptors. Heavier atoms are much less prominent in that context, and mostly limited to sulfur. Here, we report the experimental observation and theoretical study of halogen bonds to phosphorus, arsenic and antimony in the solid state. Combining 1,3,5-trifluoro-2,4,6-triiodobenzene with triphenylphosphine, -arsine, and -stibine provides cocrystals based on I···P, I···As and I···Sb halogen bonds. The demonstration that increasingly metallic pnictogens form halogen bonds sufficiently strong to enable cocrystal formation is an advance in supramolecular chemistry which opens up opportunities in materials science, as shown by colossal thermal expansion of the cocrystal involving I···Sb halogen bonds.
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Project description:Relativistic effects are found to be important for the estimation of NMR parameters in halogen-bonded complexes, mainly when they involve the heavier elements, iodine and astatine. A detailed study of 60 binary complexes formed between dihalogen molecules (XY with X, Y = F, Cl, Br, I and At) and four Lewis bases (NH3, H2O, PH3 and SH2) was carried out at the MP2/aug-cc-pVTZ/aug-cc-pVTZ-PP computational level to show the extent of these effects. The NMR parameters (shielding and nuclear quadrupolar coupling constants) were computed using the relativistic Hamiltonian ZORA and compared to the values obtained with a non-relativistic Hamiltonian. The results show a mixture of the importance of the relativistic corrections as both the size of the halogen atom and the proximity of this atom to the basic site of the Lewis base increase.
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Project description:In the hydrochloride of a pyrazolyl-substituted acetylacetone, the chloride anion is hydrogen-bonded to the protonated pyrazolyl moiety. Equimolar co-crystallization with tetrafluorodiiodobenzene (TFDIB) leads to a supramolecular aggregate in which TFDIB is situated on a crystallographic center of inversion. The iodine atom in the asymmetric unit acts as halogen bond donor, and the chloride acceptor approaches the σ-hole of this TFDIB iodine subtending an almost linear halogen bond, with Cl···I = 3.1653(11) Å and Cl···I-C = 179.32(6)°. This contact is roughly orthogonal to the N-H···Cl hydrogen bond. An analysis of the electron density according to Bader's Quantum Theory of Atoms in Molecules confirms bond critical points (bcps) for both short contacts, with ρbcp = 0.129 for the halogen and 0.321eÅ-3 for the hydrogen bond. Our halogen-bonded adduct represents the prototype for a future class of co-crystals with tunable electron density distribution about the σ-hole contact.
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