RUI: Computational Study of Vibrational Motion in Hydrogen-Bonded Systems

化学系的化学结构动力学和机制（CSDM-A）计划支持肯尼索州立大学（KSU）的Martina Kaledin教授和她的学生开发计算方法来研究氢键系统的结构和性质。 水（H2O）是氢键系统的一个例子。 当氢（H）原子与氧（O）原子结合时，H原子部分带正电，而O原子部分带负电。 在液态水中，由于不同H2O分子上的H和O之间的正负吸引力，H2O分子因此倾向于彼此粘附。 氢键实际上是许多含有O-H或N-H（N=氮）键作为其结构一部分的分子的一般特征。 氢键是一个重要的研究课题，因为它可以导致形成大的分子网络，并影响化学反应的速率和结果。 氢键的影响不容易预测，特别是当涉及许多原子和分子时。 Kaledin教授开发了先进的计算机模型来模拟氢键系统的行为和性质。 她和她的学生正在使用高性能计算机系统（KSU的IBM HPC计算机）来预测氢键系统的结构以及它们对光能的响应。 实验化学家使用所谓的光谱技术来测量不同波长的光（紫外线，可见光，红外线）如何被分子系统吸收。 Kaledin教授正在使用计算方法来预测实验“光谱”，这反过来又有助于实验科学家理解他们的观察结果。 该项目的发现有助于开发分子动力学模拟模型，从而促进我们对许多化学系统以及复杂生物系统的理解。参与该项目的研究人员包括本科生和研究生。他们正在学习超级计算，分子建模，超级计算，振动光谱的解释，分析化学反应的能量学和分子可视化技术的原理。Kaledin教授还将该研究项目的元素整合到她的正式本科课程中，旨在提高科学教育和STEM学生的成功。这些任务的核心是使用驱动分子动力学（DMD）计算和分配振动光谱。在DMD方法中，使用代表连续波（CW）激光脉冲的外部正弦电场来扫描共振光谱并获得吸收轮廓。外场的强度决定了运动的强度。DMD的一个重要特点是能够研究非谐运动和模式耦合，并进行分配。在共振频率下，弱驱动力诱导的分子运动对应于简正模频率，而较强驱动力诱导的分子运动则为非简谐运动。为了识别共振频率，在有限的驱动时间之后获得分子的平均内能。DMD也很容易扩展到二维光谱，如2D-IR，这是研究复杂动力学结构的更强大的工具。这些技术提供了质子化水分子团簇和与大气化学相关的小分子的详细动力学信息，揭示了它们的稳定性和单个原子团运动的时间尺度。参与该项目的学生正在接受分子动力学模拟、从头算和密度泛函理论计算以及拉曼和红外光谱（包括二维红外）解释的培训。 所有这些工具和技能对于进入现代劳动力市场的科学家来说都是非常有价值的。除了通过本项目中开发的计算模型推进其他科学领域外，这项工作的更广泛影响还包括促进研究界和行业之间的强有力互动，以及与来自弱势背景或代表性不足群体的学生的联系，例如，通过与Peach State Louis Stokes Alliance for Minority Participation（LSAMP）合作，该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The Chemical Structure Dynamics and Mechanism (CSDM-A) Program of the Chemistry Division supports Professor Martina Kaledin and her students at Kennesaw State University (KSU) to develop computational methods to study structure and properties of hydrogen-bonded systems. Water (H2O) is an example of a hydrogen bonded system. When hydrogen (H) atoms bond to oxygen (O) atoms, the H atom becomes partly positively charged, and the O atom partly negatively charged. In liquid water, the H2O molecules therefore tend to stick to each other because of the positive-negative attraction between H and O on different H2O molecules. Hydrogen bonding is actually a general feature of many molecules that contain O-H, or N-H (N= nitrogen) bonds as part of their structure. Hydrogen bonding is an important topic of research because it can cause the formation of large networks of molecules and influence the rates and outcome of chemical reactions. The effects of hydrogen bonding are not easy to predict, especially when many atoms and molecules are involved. Professor Kaledin has developed advanced computer models to simulate the behavior and properties of hydrogen bonded systems. She and her students are using high-performance computer systems (IBM HPC computer at KSU) are employed to predict the structure of hydrogen bonded systems as well as their response to light energy. Experimental chemists use what are called spectroscopic techniques to measure how light of different wavelengths (ultraviolet, visible, infrared) are absorbed by molecular systems. Prof. Kaledin is using computational approaches to predict experimental "spectra," which in turn helps experimental scientists understand their observations. The findings of this project are contributing to developing molecular dynamics simulation models which advance our understanding of many chemical systems, as well s complex biological systems. The researchers involved in this project include both undergraduate and graduate students. They are learning principles of supercomputing, molecular modeling, supercomputing, interpretation of vibrational spectra, analyzing the energetics of chemical reactions, and molecular visualization techniques. Prof. Kaledin is also Integrating elements of this research project into her formal undergraduate courses, with the aim to improve science education and STEM students success.Central to these tasks is to calculate and assign vibrational spectra using driven molecular dynamics (DMD). In the DMD method, an external sinusoidal electric field, representing a continuous wave (CW) laser pulse, is used to scan the spectrum for resonances and obtain an absorption profile. The strength of the external field determines the intensity of the motion. The important feature of DMD is the ability to study the anharmonic motion and mode coupling, and make assignments. At resonant frequencies, the molecular motions induced by weak driven force correspond to the normal-mode frequencies, while harder driving induces anharmonic motion. To identify resonant frequencies, the average internal energy of the molecule is obtained after a finite time of driving. DMD is also easily expandable to two-dimensional spectroscopy, such as 2D-IR, an even more powerful tool for studying complex dynamical structures. These techniques provide detailed dynamic information on protonated water clusters and small molecules relevant to atmospheric chemistry, reveal their stability and timescale of motion of individual groups of atoms. The students involved in this project are being trained in molecular dynamics simulations, ab initio and density functional theory calculation, and interpretation of Raman and infrared spectra (including 2D IR). All of these tools and skills are highly valuable for scientists entering the modern workforce. In addition to advancing other areas of science through the computational models developed in this project, the broader impacts of this work is includes the promotion of strong interactions between the research community and industry, and outreach to students from disadvantaged backgrounds or underrepresented groups, for example through engagement with the Peach State Louis Stokes Alliances for Minority Participation (LSAMP).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.