Aleman Carlos, Zanuy David, Casanovas Jordi, Cativiela Carlos, Nussinov Ruth
Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
J Phys Chem B. 2006 Oct 26;110(42):21264-71. doi: 10.1021/jp062804s.
We have used quantum mechanical calculations at the B3LYP/6-311G(d,p) level to determine the conformational preferences of the N-acetyl-N'-methylamide derivative of 1-aminocyclopentane-1-carboxylic acid in the gas phase, chloroform solution, and water solution. The backbone conformation of this dipeptide has been described through the dihedral angles varphi and psi, while the pseudorotational phase angle was used to define the conformation of the cyclopentane ring. Results indicate that the backbone flexibility of this amino acid is restricted by the cyclic nature of the side chain, the relative stability of the different conformations depending on the polarity of the environment. The potential energy of the pseudorotation was also studied as a function of the backbone conformation. Interestingly, the conformation of the cyclic side chain depends on the backbone arrangement. Furthermore, the number of pseudorotational states accessible at room temperature is high in all the investigated environments, especially in aqueous solution. Finally, a set of force-field parameters for classical molecular mechanics calculations was developed for the investigated amino acid. Molecular dynamics simulations in both chloroform and aqueous solutions were performed to demonstrate the reliability of such parameters.
我们已使用B3LYP/6-311G(d,p)水平的量子力学计算来确定1-氨基环戊烷-1-羧酸的N-乙酰基-N'-甲基酰胺衍生物在气相、氯仿溶液和水溶液中的构象偏好。该二肽的主链构象通过二面角φ和ψ来描述，而假旋转相角用于定义环戊烷环的构象。结果表明，该氨基酸的主链柔韧性受到侧链环状结构的限制，不同构象的相对稳定性取决于环境的极性。还研究了假旋转的势能作为主链构象的函数。有趣的是，环状侧链的构象取决于主链排列。此外，在所有研究的环境中，尤其是在水溶液中，室温下可及的假旋转状态数量很高。最后，为所研究的氨基酸开发了一组用于经典分子力学计算的力场参数。在氯仿和水溶液中进行了分子动力学模拟，以证明这些参数的可靠性。
