Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454-9110, USA.
J Chem Phys. 2012 Feb 28;136(8):084109. doi: 10.1063/1.3688228.
As the dominant physiological solvent, water drives the folding of biological macromolecules, influences conformational changes, determines the ionization states of surface groups, actively participates in catalytic events, and provides "wires" for long-range proton transfer. Elucidation of all these roles calls for atomistic simulations. However, currently available methods do not lend themselves to efficient simulation of proton transfer events, or even polarizability and flexibility. Here, we report that an explicit account of valency can provide a unified description for the polarizability, flexibility, and dissociability of water in one intuitive and efficient setting. We call this approach LEWIS, after the chemical theory that inspires the use of valence electron pairs. In this paper, we provide details of the method, the choice of the training set, and predictions for the neat ambient liquid, with emphasis on structure, dynamics, and polarization. LEWIS water provides a good description of bulk properties, and dipolar and quadrupolar responses.
作为主要的生理溶剂,水驱动生物大分子的折叠,影响构象变化,决定表面基团的离解状态,积极参与催化事件,并为长程质子转移提供“导线”。要阐明所有这些作用都需要原子模拟。然而,目前可用的方法并不适合于有效地模拟质子转移事件,甚至不适合于极化率和柔韧性。在这里,我们报告说,价的明确说明可以在一个直观和有效的设置中为水的极化率、柔韧性和离解性提供统一的描述。我们将这种方法称为 LEWIS,以启发使用价电子对的化学理论命名。在本文中,我们提供了该方法的详细信息、训练集的选择以及对纯净环境液体的预测,重点是结构、动力学和极化。LEWIS 水对体相性质、偶极和四极响应提供了很好的描述。