从原子到大分子体系的计算机模拟--计算化学50年
With Computers from Atoms to Macromolecular Systems

Clementi Enrico ¹ ^* Corongiu Giorgina ²

文摘	本文综述并修订了从20世纪50年代末至今，我们在计算化学领域所做的一些有意义的工作。序言部分把我们的工作置于当代科学的背景之下。然后我们以一种经典的基准测试体系--一种新的单粒子表象(即替代传统的原子和分子自旋轨道的化学自旋轨道)所构建的氢分子(H~2)波函数--作为开始。用Hartree-Fock-Heitler-London(HF-HL)对从双原子分子到小的多原子分子进行计算所得的结果，与用传统的Hartree-Fock(HF)和Heitler-London(HL)计算的结果进行了对比；我们推断出，使用HF-HL水平的解决方案是计算量子化学的一个通用而且合理的选择。此外，我们也指出用化学自旋轨道构建的波函数，与HF-HL模型所得的波函数是等同的。除了这些计算之外，我们还对相关能、威格纳(Wigner)和库仑空穴(Coulomb Hole)泛函进行了评判性分析。上述研究工作是Hartree-Fock早期工作的继承与发展，这一时期以对原子和分子体系的先驱性计算为特征，包括基组优化、在HF和后HF(post Hartree-Fock)方法水平上的原子能量表格化以及用超级分子方法获得势能面。但是，要处理大分子体系并清楚地考察温度和时间，我们必须改用统计方法；我们回顾了用蒙特卡罗(Monte Carlo)、分子动力学和朗之万(Langevin)动力学，首先针对平衡的体系，而后在非平衡的开放体系中的模拟。对把这些模型联合起来建立的全局模拟法，也进行了详细的讨论。以上所有的工作既需要计算机硬件，也需要应用于计算化学各分支的程序。本文重温了过去半个世纪中人们编写、存档、免费发布的量子化学原子和分子程序以及统计力学程序。也回顾了20世纪80年代初，我们在设计和组装并行性超级计算机架构方面所做的先驱性工作，这些工作实现了计算化学上的第一个大规模并行计算。
其他语种文摘	We review and update selected contributions to computational chemistry made since the late 1950s.Introductory remarks are given to place our work in the context of contemporary science.We start with a classical benchmark, the H~2 wave-function constructed with a new one-particle representation, the Chemical spin-Orbitals, which replaces the traditional Atomic and Molecular spin-Orbitals.Computations from diatomic to small polyatomic molecules, obtained with the Hartree-Fock-Heitler-London(HF-HL)model, are compared to those obtained from the traditional Hartree-Fock(HF)and Heitler-London(HL)methods; we conclude that the hierarchy of solutions within the HF-HL approach represents a general and reasonable choice for computational quantum chemistry.Further, we show that a wave function constructed with Chemical spin-Orbitals is equivalent to a wave-function obtained with the HF-HL model.These simulations are complemented with a critical analysis on the correlation energy, and on Wigner and Coulomb Hole functionals. The above studies follow the early Hartree-Fock period(1960-1970)characterised by pioneering computations on atomic and molecular systems, including basis set optimisation, atomic energy tabulation at the Hartree-Fock and post Hartree-Fock level, and potential energy surface computations obtained with the supermolecular approach.However, to deal with large molecular systems and to explicitly consider temperature and time, we must turn to statistical methods; we recall simulations using Monte Carlo, Molecular Dynamics, and Langevin dynamics, first at equilibrium, then for open systems at non-equilibrium.A concatenation of these models constitutes to the Global Simulation approach, discussed in detail. The above work requires both computer hardware and application codes in different areas of computational chemistry.We recall the quantum chemical atomic and molecular codes and the statistical mechanics codes written, documented and freely distributed for the last half century.Further, we recall our pioneering efforts in the early 1980s in computer architecture, with the design and assembly of a parallel supercomputer extensively used to perform the first parallel applications in computational chemistry.
来源	化学进展 ,2011,23(9):1795-1830 【核心库】
关键词	全局模拟 ; 量子化学 ; 平衡和非平衡动力学 ; 生物分子 ; 计算机设计 ; 并行性
地址	1. Via Carloni 38,Italy, Italy, Como, 22100 2. Dipartimento di Scienze Chimiche e Ambientali, Universitàdell'Insubria,Italy, Italy, Como, 22100
语种	中文
文献类型	研究性论文
ISSN	1005-281X
学科	化学
文献收藏号	CSCD:4346979