Theoretical Study Of The Nature Of The Organic Fluorine Hydrogen Bond In Molecular Crystals

In recent years, the achievement of fluorination in improving molecularproperties and building supramolecular assemblies has been remarkable. Due to thehighly polarization of the C–F bond, fluorine containing compounds exhibit a highthermal stability and oxidative stability, weak intermolecular interactions and a smallsurface tension compared to hydrocarbons. These beneficial effects are utilized invarious fields of solid state reaction, catalytic, crystal, dyes, membrane, conductivepolymer complexes, pharmaceutical and agricultural chemicals. However, thenon-covalent chemistry organic fluorine involved is still in the primary stage ofcognition. Some of its most simple aspects have not been well understand. Forinstance, whether organic fluorine can form a hydrogen bond is controversial.Row et al. have structurally identified intermolecular C H···F C interaction incrystalline but-2-yne-1,4-diyl bis(2,3,4,5,6-pentafluorophenyl-carbonate)1, but-2-yne-1,4-diyl bis(4-fluorophenylcarbonate)2, and but-2-yne-1,4-diyl bis(2,3,4,5,6-pentafluorophenylcarbamate)3. Interestingly, one of shortest C H···F C distancesreported till date was found in crystalline1based on neutron diffraction. In addition,the organic molecule1has a preference for syn-conformation in its crystalline state.Their study provides an opportunity to further explore the C H···F C interactionsbeyond the criteria of mere geometry.In this paper, we have theoretically characterized these organic fluorinehydrogen bond interactions using atoms in molecule (AIM) and natural bond orbitalanalysis (NBO). Considering the importance of the London dispersion interactions,dispersion-corrected DFT was used to study C–H···F C hydrogen bonds.B97D/6-311++G(d,p) was used to optimize the crystal structure. The main work andthe conclusions are as follows: First, the calculation study about C–H···F–C interactions, based on the crystallinestructures of1~3, was performed in gas-phase at the B97D/6-311++g(d,p) level. AIManalyses show that the ρbvalues at H···F BCPs and the values of the Laplacian▽2ρbdo well lie in the classic or typical quantity for hydrogen bond, from0.002to0.035a.u. in ρband from0.020to0.139a.u. in▽2ρb. The comparative study further revealsthat the C–H···F–C hydrogen bond studied here is weak although the distance of H···Fin crystalline1is extremely short and even close to the H···O distance in N–H···O=Chydrogen bond. Calculated interaction energy (0.82kcal/mol) of C–H···F–C hydrogenbond in crystalline1supports this result. The C–H···F–C hydrogen bonds incrystalline1,2, and3are mainly closed-shell. Additionally, NBO analyses indicatethat charge transfer (nF�'σ*C–H) is significant even for such weak C–H···F–Chydrogen bonds studied here. The significantly large CT stabilizing role in crystalline1compared with crystalline2and3rationalizes the preference for thesyn-conformation of the molecule1.Second, based on the above study, we choose the system of η-1,2,3,4,5,6-hexafluorocyclohexane (benzenehexafluoride) of O’Hagan’s research. AIM analysesshow that the ρbvalues at H···F BCPs range between0.0066a.u. and0.0135a.u., andthat the values of the Laplacian▽2ρblie between0.0062–0.0094a.u. and0.0250–0.0342a.u. These values lie in the range for the existence of hydrogen bond, from0.002to0.035a.u. in ρband0.020to0.139a.u. in▽2ρb. These interactions presenttypical properties of closed-shell interactions: the value of electron density, ρbisrelatively low; the ratio of the perpendicular contractions of ρbto its parallelexpansion|λ1|/λ3is <1, and the Laplacian of the electron density,▽2ρbis positive.NBO analyses indicate that charge transfer phenomena (nF�'σ*C–H) issignificant in these C–H···F–C hydrogen bonds. In addition, the second-orderperturbation energies of C9–H15···F21C27and C29–H35···F4C10are1.03and1.06kcal/mol, respectively. To estimate the magnitude of these C–H···F–C interactions,Wiberg bond indices were calculated. The bond indexs for C8–H14···F22C28,C10–H16···F22C28and C9–H15···F22C28are0.0015,0.0013and0.0018, respectively. The strongest interaction C29–H35···F4C10was found to be0.0059. Compared withthe H···F hydrogen bond in the HF dimer (with a bond index of0.0296), these valuesoccupies only5–20%of this value.