RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I
RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I
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DOI：
10.1002/jcc.20425
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发表时间：
2006-07-30
影响因子：
3
通讯作者：
Stewart, James J. P.
中科院分区：
文献类型：
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作者：
Rocha, Gerd B.;Freire, Ricardo O.;Stewart, James J. P.
20年前，具有里程碑意义的AM1被引入，由于其一贯的良好结果和经过时间考验的可靠性，目前在无数计算量子化学程序中可用，因此在化学家中拥有越来越广泛的追随者。然而，半经验分子轨道模型仍然是有限的准确性，需要改进，如果要实现新的线性标度技术，如MOZYME和LocalSCF的全部潜力。因此，在这篇文章中，我们提出RM 1（累西腓模型1）：AMI的重新参数化。如前所述，参数化过程中使用的属性是：生成热，偶极矩，电离势和几何变量（键长和键角）。考虑到绝大多数对生命有重要意义的分子可以只用六种元素组装：C、H、N、O、P和S，并且通过添加卤素，我们现在可以构建大多数对药物研究有重要意义的分子，我们的训练集由1736个分子组成，代表有机和生物化学，包含C、H、N、O、P、S、F、Cl、Br和I原子。与AM1不同，与PM3类似，所有RM1参数都已优化。对于形成，偶极矩，电离势，和原子间距离，RM1的平均误差，为1736个分子，小于AMI，PM3，和PM5。实际上，以千卡（.）对于AMI、PM3和PM5，生成的摩尔比为11.15、7.98和6.03，而对于RMI，该值为5.77。AMI、PM3、PM5和RMI的偶极矩的德拜误差分别为0.37、0.38、0.50和0.34。同样，电离势的误差（eV）分别为0.60、0.55、0.48、0.45，原子间距离的误差（埃）分别为0.036、0.029、0.037、0.027。RM1的键角平均误差为6.82度，仅略高于AMI的5.88度，且均远小于PM3和PM5的6.98度和9.83度。此外，在RMI中校正了PM3氮充量中的已知误差。因此，RMI代表了对AMI及其类似的后继者PM3的改进，并且可能与PM5非常有竞争力，PM5是一个有点不同的模型，并且没有完全公开。RMI具有与AM I相同的分析构造和每个原子的相同数量的参数，因此可以在已经具有AM I的任何软件中容易地实现，而不需要任何代码行的任何改变，唯一的例外是参数本身的值。
Twenty years ago, the landmark AM1 was introduced, and has since had an increasingly wide following among chemists due to its consistently good results and time-tested reliability-being presently available in countless computational quantum chemistry programs. However, semiempirical molecular orbital models still are of limited accuracy and need to be improved if the full potential of new linear scaling techniques, such as MOZYME and LocalSCF, is to be realized. Accordingly, in this article we present RM1 (Recife Model 1): a reparameterization of AMI. As before, the properties used in the parameterization procedure were: heats of formation, dipole moments, ionization potentials and geometric variables (bond lengths and angles). Considering that the vast majority of molecules of importance to life can be assembled by using only six elements: C, H, N, O, P, and S, and that by adding the halogens we can now build most molecules of importance to pharmaceutical research, our training set consisted of 1736 molecules, representative of organic and biochemistry, containing C, H, N, 0, P, S, F, Cl, Br, and I atoms. Unlike AM1, and similar to PM3, all RM1 parameters have been optimized. For enthalpies of formation, dipole moments, ionization potentials, and interatomic distances, the average errors in RM1, for the 1736 molecules, are less than those for AMI, PM3, and PM5. Indeed, the average errors in kcal(.)mol(-1) of the enthalpies of formation for AMI, PM3, and PM5 are 11.15, 7.98, and 6.03, whereas for RMI this value is 5.77. The errors, in Debye, of the dipole moments for AMI, PM3, PM5, and RMI are, respectively, 0.37, 0.38, 0.50, and 0.34. Likewise, the respective errors for the ionization potentials, in eV, are 0.60, 0.55, 0.48, and 0.45, and the respective errors, in angstroms, for the interatomic distances are 0.036, 0.029, 0.037, and 0.027. The RM1 average error in bond angles of 6.82 degrees is only slightly higher than the AMI figure of 5.88 degrees, and both are much smaller than the PM3 and PM5 figures of 6.98 degrees and 9.83 degrees, respectively. Moreover, a known error in PM3 nitrogen charges is corrected in RMI. Therefore, RMI represents an improvement over AMI and its similar successor PM3, and is probably very competitive with PM5, which is a somewhat different model, and not fully disclosed. RMI possesses the same analytical construct and the same number of parameters for each atom as AM I, and, therefore, can be easily implemented in any software that already has AM I, not requiring any change in any line of code, with the sole exception of the values of the parameters themselves.