{"title":"甲烷-水笼的量子化学分子动力学模拟","authors":"Giuseppe Lanza","doi":"10.1002/qua.27487","DOIUrl":null,"url":null,"abstract":"<p>The dynamic stability of various methane-water clathrate-like cages (CH<sub>4</sub>@(H<sub>2</sub>O)<sub><i>n</i></sub>, <i>n</i> = 16, 18, 20, 22), has been analyzed explicitly considering thermal effects by means of ab initio M06-2X/6–31+G*/PCM calculations, which make use of Gaussian basis functions. Starting from the equilibrium filled cage structures, <i>classical</i>, dynamic reaction coordinate (DRC) on the Born–Oppenheimer surface, and <i>semiclassical</i>, Born–Oppenheimer plus harmonic zero-point energy surface (BOMD), molecular dynamics have been carried out. Water molecules have a high tendency to orient covalent O–H bonds tangentially to the hydrophobic surface, thus clathrate-like arrangements are an acceptable model to fully hydrate methane. If the cage size is such as to minimize core repulsion, due to electron cloud overlap, and to maximize host–guest van der Waals attractions, the clathrate-like structures have a life-time of two picoseconds in <i>classical</i> DRC simulations. The inclusion of quantum kinetic energy in BOMD simulations results in less structured cages with a reduced amount of hydrogen bond network. The preferential tangential orientation of the O-H bonds is largely maintained, although few of them point toward the methane for a very short time in BOMD simulations. The reduced configurational space of water molecules hydrating hydrophobic moiety is highlighted, thus any satisfactory molecular modeling has to account for it.</p>","PeriodicalId":182,"journal":{"name":"International Journal of Quantum Chemistry","volume":null,"pages":null},"PeriodicalIF":2.3000,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/qua.27487","citationCount":"0","resultStr":"{\"title\":\"Quantum Chemical Molecular Dynamics Simulations for Methane-Water Cages\",\"authors\":\"Giuseppe Lanza\",\"doi\":\"10.1002/qua.27487\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>The dynamic stability of various methane-water clathrate-like cages (CH<sub>4</sub>@(H<sub>2</sub>O)<sub><i>n</i></sub>, <i>n</i> = 16, 18, 20, 22), has been analyzed explicitly considering thermal effects by means of ab initio M06-2X/6–31+G*/PCM calculations, which make use of Gaussian basis functions. Starting from the equilibrium filled cage structures, <i>classical</i>, dynamic reaction coordinate (DRC) on the Born–Oppenheimer surface, and <i>semiclassical</i>, Born–Oppenheimer plus harmonic zero-point energy surface (BOMD), molecular dynamics have been carried out. Water molecules have a high tendency to orient covalent O–H bonds tangentially to the hydrophobic surface, thus clathrate-like arrangements are an acceptable model to fully hydrate methane. If the cage size is such as to minimize core repulsion, due to electron cloud overlap, and to maximize host–guest van der Waals attractions, the clathrate-like structures have a life-time of two picoseconds in <i>classical</i> DRC simulations. The inclusion of quantum kinetic energy in BOMD simulations results in less structured cages with a reduced amount of hydrogen bond network. The preferential tangential orientation of the O-H bonds is largely maintained, although few of them point toward the methane for a very short time in BOMD simulations. The reduced configurational space of water molecules hydrating hydrophobic moiety is highlighted, thus any satisfactory molecular modeling has to account for it.</p>\",\"PeriodicalId\":182,\"journal\":{\"name\":\"International Journal of Quantum Chemistry\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.3000,\"publicationDate\":\"2024-09-23\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/qua.27487\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"International Journal of Quantum Chemistry\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/qua.27487\",\"RegionNum\":3,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"International Journal of Quantum Chemistry","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/qua.27487","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0
摘要
通过使用高斯基函数进行 ab initio M06-2X/6-31+G*/PCM 计算,明确分析了各种甲烷-水凝胶笼(CH4@(H2O)n,n = 16、18、20、22)的动态稳定性,其中考虑到了热效应。从平衡填充笼结构开始,进行了经典的、博恩-奥本海默表面上的动态反应坐标(DRC)和半经典的、博恩-奥本海默加谐波零点能表面(BOMD)的分子动力学计算。水分子非常倾向于将共价 O-H 键定向到与疏水表面相切的方向,因此类似于凝胶体的排列是完全水合甲烷的可接受模型。如果笼子的大小能够使电子云重叠造成的核心排斥力最小化,并使主客范德华吸引力最大化,那么在经典的 DRC 模拟中,类凝胶结构的寿命为两皮秒。在 BOMD 模拟中加入量子动能后,笼状结构的氢键网络数量减少。在 BOMD 模拟中,虽然很少有 O-H 键在很短的时间内指向甲烷,但 O-H 键的优先切向取向基本保持不变。水分子水合疏水分子的构型空间缩小的问题凸显出来,因此任何令人满意的分子建模都必须考虑到这一点。
Quantum Chemical Molecular Dynamics Simulations for Methane-Water Cages
The dynamic stability of various methane-water clathrate-like cages (CH4@(H2O)n, n = 16, 18, 20, 22), has been analyzed explicitly considering thermal effects by means of ab initio M06-2X/6–31+G*/PCM calculations, which make use of Gaussian basis functions. Starting from the equilibrium filled cage structures, classical, dynamic reaction coordinate (DRC) on the Born–Oppenheimer surface, and semiclassical, Born–Oppenheimer plus harmonic zero-point energy surface (BOMD), molecular dynamics have been carried out. Water molecules have a high tendency to orient covalent O–H bonds tangentially to the hydrophobic surface, thus clathrate-like arrangements are an acceptable model to fully hydrate methane. If the cage size is such as to minimize core repulsion, due to electron cloud overlap, and to maximize host–guest van der Waals attractions, the clathrate-like structures have a life-time of two picoseconds in classical DRC simulations. The inclusion of quantum kinetic energy in BOMD simulations results in less structured cages with a reduced amount of hydrogen bond network. The preferential tangential orientation of the O-H bonds is largely maintained, although few of them point toward the methane for a very short time in BOMD simulations. The reduced configurational space of water molecules hydrating hydrophobic moiety is highlighted, thus any satisfactory molecular modeling has to account for it.
期刊介绍:
Since its first formulation quantum chemistry has provided the conceptual and terminological framework necessary to understand atoms, molecules and the condensed matter. Over the past decades synergistic advances in the methodological developments, software and hardware have transformed quantum chemistry in a truly interdisciplinary science that has expanded beyond its traditional core of molecular sciences to fields as diverse as chemistry and catalysis, biophysics, nanotechnology and material science.