Alemán C, Casanovas J, Galembeck S E
Departament d'Enginyeriía Química, E.T.S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Barcelona, Spain.
J Comput Aided Mol Des. 1998 May;12(3):259-73. doi: 10.1023/a:1007908630431.
The suitability of ab initio, semiempirical and density functional methods as sources of stretching and bending parameters has been explored using the PAPQMD (Program for Approximate Parametrization from Quantum Mechanical Data) strategy. Results show that semiempirical methods provide parameters comparable to those compiled on empirical force fields. In this respect the AMI method seems to be a good method to obtain parameters at a minimum computational cost. On the other hand, harmonic force fields initially developed for proteins and DNA have been extended to include compounds containing highly strained three-membered rings, like 1-aminocyclopropane-1-carboxylic acid. For this purpose the cyclopropyl ring has been explicitly parametrized at the AMI level considering different chemical environments. Finally, the new set of parameters has been used to investigate the conformational preferences of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid. Results indicate that such compounds tend to adopt a helical conformation stabilized by intramolecular hydrogen bonds between residues i and i + 3. This conformation allows the arrangement of the cyclic side chains without steric clashes.
利用PAPQMD（从量子力学数据进行近似参数化的程序）策略，研究了从头算、半经验和密度泛函方法作为伸缩和弯曲参数来源的适用性。结果表明，半经验方法提供的参数与根据经验力场汇编的参数相当。在这方面，AMI方法似乎是以最低计算成本获得参数的良好方法。另一方面，最初为蛋白质和DNA开发的简谐力场已扩展到包括含有高度张力三元环的化合物，如1-氨基环丙烷-1-羧酸。为此，考虑到不同的化学环境，在AMI水平上对环丙基环进行了明确的参数化。最后，使用新的参数集研究了由1-氨基环丙烷-1-羧酸构成的同肽的构象偏好。结果表明，这类化合物倾向于采取由i和i + 3残基之间的分子内氢键稳定的螺旋构象。这种构象允许环状侧链排列而无空间位阻冲突。
