基于周期性边界条件的分块量子化学方法对液态水的从头算分子动力学模拟

本文利用分块量子化学方法,实现了在周期性边界条件下应用二阶微扰(MP2)理论对液态水的从头算分子动力学模拟. 通过采用aug-cc-pVDZ基组,MP2理论可以精确地描述水分子之间的相互作用势能面,因而在描述水的各项理化性质方面,MP2有望提供比密度泛函理论更加精确的结果. 本研究计算了多种水的结构及动力学性质,包括径向分布函数,扩散系数,偶极矩,三个临近氧原子的角度分布,氢键结构,都得到了与实验观测一致的结果. 因此,周期性边界量子分块方法可以作为一种研究水的物质结构的可靠理论方法,并且有望促进水科学领域争议性问题的解决. 同时,该方法具有普适性和可扩展性,为有效应用高精度量子化学从头算方法计算其他凝聚态体系提供了理论框架.     

神奇的隐声斗篷

"隐声斗篷"是一种新型的隔音材料,它能使入射声波沿斗篷表面无反射地绕行,从而对斗篷保护下的物体产生"隐声"效果。美国杜克大学的Steven Cummer博士等人在研究中发现光学隐身的数学原理同样适用于声波,从而提出了隐声斗篷     

CO分子在肌红蛋白结合口袋的QM/MM动力学模拟

Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide (CO) in the heme distal pocket (named as B₁ and B₂ states) of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B₁ and B₂ states correspond to Fe…CO (with carbon atom closer to iron center of heme) and Fe…OC (with oxygen atom closer to Fe), by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B₁ and B₂ is 13.1 cm^-1, which is in good agreement with experimental value of 11.5 cm^-1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein. From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues (namely, HIS64, ILE107, and PHE43). This study provides new physical insights on rational design of enzyme with higher electric field at the active site.