以间苯二甲酸为原料,经过多步合成了1种含偶氮苯和1,3,4-噁二唑基团化合物5-[4-(十六烷氧基)苯基偶氮-]1,3-苯基-二-(1,3,4-噁二唑硫基)乙酸甲酯(8),利用IR、UV-vis、1 H NMR对其结构进行表征.该化合物四氢呋喃溶液紫外光谱中,偶氮苯结构K带的最大吸收波长为360nm,摩尔吸光系数ε为27 476L.mol-1.cm-1.在365nm紫外光照射下,偶氮苯基团发生反-顺异构化,照射5min后达到光稳态,光稳态时偶氮苯基团光致反顺异构化速率常数kp为1.338 9min-1,反式异构体转化效率R为80.95%,顺式异构体比例Y为84.99%,光稳态时偶氮苯K带最大吸收波长由360nm蓝移至326nm,将其置于暗室中,35h后恢复到光照前状态.
The binding energies of thirty-six hydrogen-bonded peptide-base complexes, including the peptide backbone-ase complexes and amino acid side chain-base complexes, are evaluated using the analytic potential energy function established in our lab recently and compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparison indicates that the analytic potential energy function yields the binding energies for these complexes as reasonable as MP2 does, much better than the force fields do. The individual N H…O=C, N H…N, C H…O=C, and C H…N attractive interaction energies and C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interaction energies, which cannot be easily obtained from ab initio calculations, are calculated using the dipole-dipole interaction term of the analytic potential energy function. The individual N H…O=C, C H…O=C, C H…N attractive interactions are about 5.3±1.8, 1.2±0.4, and 0.8 kcal/mol, respectively, the individual N H … N could be as strong as about 8.1 kcal/mol or as weak as 1.0 kcal/mol, while the individual C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interactions are about 1.8±1.1, 1.7±0.6, 0.6±0.3, and 0.35±0.15 kcal/mol. These data are helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies.
Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites （Site 1, Site 2, and Site 3） that can induce strong directional N-H...O=C hydrogen bonding interaction. In this paper, theoretical calculations are carded out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil （or thymine） would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers.
