Theoretical and Computational Biomolecular Physics Group, Department of Physics, Purdue University, West Lafayette, IN 47907, USA.
Phys Chem Chem Phys. 2012 Mar 14;14(10):3414-24. doi: 10.1039/c2cp23673g. Epub 2012 Feb 2.
The computation of intermolecular interaction energies via commonly used density functionals is hindered by their inaccurate inclusion of medium and long range dispersion interactions. Practical computation of inter- and intra-macrobiomolecule interaction energies, in particular, requires a fairly accurate yet not overly expensive methodology. It is also desirable to compute intermolecular energies not only at their equilibrium (lowest energy) configurations but also over a range of biophysically relevant distances. We present a method to compute intermolecular interaction energies by including an empirical correction for dispersion which is valid over a range of intermolecular distances. This is achieved by optimizing parameters that moderate the empirical correction by explicit comparison of density functional (B3LYP) energies with distance-dependent (DD) reference values obtained at the CCSD(T)/CBS limit. The resulting method, hereafter referred to as B3LYP-DD, yields interaction energies with an accuracy generally better than 1 kcal mol(-1) for different types of noncovalent complexes, over a range of intermolecular distances and interaction strengths, relative to the expensive CCSD(T)/CBS standard. For a training set of dispersion interacting complexes, B3LYP-DD interaction energies in combination with diffuse functions display absolute errors equal to or smaller than 0.68 kcal mol(-1). The empirical correction does not significantly increase the computational cost as compared to standard density functional calculations. Applications relevant to biomolecular energy and structure, such as prediction of DNA base-pair interactions, are also presented.
通过常用密度泛函计算分子间相互作用能受到其对中长程色散相互作用不准确包含的限制。特别是,计算分子间和宏观生物分子相互作用能需要相当准确但不过于昂贵的方法。还希望不仅在其平衡(最低能量)构象下而且在一系列与生物物理相关的距离上计算分子间能量。我们提出了一种通过包括对色散的经验校正来计算分子间相互作用能的方法,该方法在一系列分子间距离上有效。这是通过优化参数来实现的,这些参数通过明确比较密度泛函(B3LYP)能量与在 CCSD(T)/CBS 极限下获得的距离相关(DD)参考值来调节经验校正。该方法,此后称为 B3LYP-DD,与昂贵的 CCSD(T)/CBS 标准相比,对于不同类型的非共价复合物,在一系列分子间距离和相互作用强度范围内,具有通常优于 1 kcal mol(-1)的精度,用于不同类型的非共价复合物。对于一组具有色散相互作用的复合物的训练集,B3LYP-DD 相互作用能与弥散函数结合显示的绝对误差等于或小于 0.68 kcal mol(-1)。与标准密度泛函计算相比,经验校正不会显著增加计算成本。还介绍了与生物分子能量和结构相关的应用,例如 DNA 碱基对相互作用的预测。