Nitrogen-containing Supramolecular Crystals And Theoretical Study Based On Hydrogen Bonding

Supramolecular chemistry is highly interdisciplinary based on non-covalent interactions as the driving force and recent years have witnessed its rapid and energetic development. Among the non-covalent interactions, hydrogen bonding has been called ‘‘universal role in supermolecule’’ and the most common ‘‘tool’’ in crystal engineering due to its strength, directionality and predictability. Small organic molecules containing complementary functional groups are employed as tectons and building blocks to synthesize organic crystalline material with specific structures through supramolecular self-assembly and hydrogen-bonding interactions, which can provide important structure information for the study of various material properties. Thus, it become an active area in supramolecular chemistry in recent years. In this doctoral dissertation, we have synthesized five series of supramolecular compounds by conventional solution or solvothermal method, taking Bronsted acids(HA) and bases(B) as the main raw material. We systematically studied their crystal structure, calculated the charge distribution, electrostatic potential and proton affinities of base components in the supramolecular system by the use of the B3 LYP method from density functional theory, estimated the p Ka of reaction components based on Marvin Sketch software, predicted and interpreted experimental results from the theory. The main contents are as follows:First, different primary amines reacted with 3,5-dinitro-benzoic acid, which have complementary functional groups –NH2 and –COOH, preparing three supramolecular salts and one co-crystal. The p Ka values well explain why compounds 1-3 are supramolecular salts but 4 is a neutral co-crystal. Quantum chemical calculations show the ability to accept a proton and amino group is the protonated amine site. 1 and 2 possess similar crystal structures, in which hydrogen-bonding chains form between carboxyl anions and amine cations. No such similar structures are found in 3 and 4 but the shape of a Chinese knot among four amine cations and single chain are observed, respectively. Thus, the slight change of amine components will have an influence on the crystal structure of final products.Second, three supramolecular salts have been obtained based on the secondary 2,2’-dipyridylamine. The charge distribution and electrostatic potential indicate the nitrogen atoms from pyridine as the protonated sites instead of the secondary amine in the middle, which is consistent with experimental results. The secondary amine bears two very close basic sites and upon protonation the intramolecular S(6) ring will be afforded through hydrogen bond N–H+···N. Therefore, it can be used as a proton sponge. Moreover, proton affinity of 2,2’-dipyridylamine is 247.72 kcal·mol-1(more than 245 kcal·mol-1), so it belongs to the superbase. Although different aromatic acids also change the crystal structure of final products, they do not affect the intramolecular hydrogen bonds in amine cations.Third, aliphatic carboxylic acids, D- and L-tartaric acid, have been chosen to react with 1-(2-pyrimidyl)piperazine, producing two highly similar crystals. By charge distribution and electrostatic potential of the piperazine, combined with the p Ka of each component, we predict that single proton transfer will occur in the reaction and nitrogen atom from piperazine is more easily protonated than that in pyrimidine. Indeed, crystal structure analysis confirmed this speculation. Thermal analysis revealed that the two salts undergo an irreversible phase transition at about 158 and 175 ℃, which are attributed to the loss of water molecule and melting point, respectively. The temperature- and frequency-dependent dielectric constants suggested a low-frequency thermal fluctuation above 80 ℃. The introduction of enantiomeric D- and L-tartaric acid made the two compounds crystallize in the chiral space group P212121, but their ferroelectric behavior were not obvious at room temperature.Furthermore, we explored the effect of different inorganic acids(HNO3,H3PO4,HI,HPF6,HBF4å'Œ H2SO4) on bent dipyridines(2,5-bis(4-pyridyl)-1,3,4-oxadiazole) in supramolecular assemblies. Seven supramolecular salt were synthesized, assisted by different inorganic anions(NO3-,HPO42-,I3-/I-,PF6-,BF4-å'Œ SO42-), topologies of which act as the dominant factor in the crystallization process and induce the formation of diverse supramolecular architectures through hydrogen bonds, anion···π and π···π interactions. Calculations of charge distribution, electrostatic potential and proton affinity for dipyridines expand the understanding of supramolecular assemblies in reaction systems.Finally, pyridine-based 1-(4-pyridyl)piperazine and 4-pyrrolidinopyridine have been utilized to construct supermolecules together with a variety of inorganic acids(HCl,HBr,HI,HNO3,HCl O4,HIO4,H2SO4å'Œ H3PO4). However, only four tetrahedral anion-assisted supramolecular salts were obtained(H2PO4–,Cl O4–å'Œ IO4–), indicating that the two pyridine-based compounds are prone to cocrystallize with tetrahedral oxyanions and the larger and more charge-diffuse anions are generally preferred. The p Ka calculations confirmed that inorganic acids are strong enough to protonate base components and make compound 1-4 in the form of supramolecular salts. Related calculations by density function theory reveal that it is much more difficult for diprotonation than monoprotonation.In summary, we have synthesized a variety of supramolecular compounds based on hydrogen bonding, including supramolecular systems of aromatic carboxylic acids with primary amines, aromatic acids with secondary amines, aliphatic carboxylic acids with 1-(2-pyrimidyl)piperazine to inorganic acid with pyridine-based compounds. We explore characteristics and rules of these supermolecules related to crystal engineering by the systematical analysis of crystal structures combined with theoretical calculations.