The Local Mode Analysis - Decoding Chemical Information From Vibrational Spectroscopy Data

局域模式分析 - 从振动光谱数据中解码化学信息

• 批准号: 2102461
• 负责人: Elfi Kraka
• 金额: $ 49.8万
• 依托单位: Southern Methodist University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2102461&HistoricalAwards=false
• 关键词: Local; Mode; Analysis; Decoding; Chemical

In this project funded by the Chemical Structure Dynamics and Mechanisms-A (CSDM-A) Program of the Chemistry Division, Professor Elfi Kraka and her Computational and Theoretical Chemistry Group (CATCO) at Southern Methodist University (SMU) will use vibrational spectroscopy data to gain new insights on molecules. Over the past decades, vibrational spectroscopy has developed into an important analytical tool with ample applications in chemical synthesis, biological assays, materials quality control, forensic science, or the health sector. Infrared (IR) light has the proper energy to excite vibrations in a molecule. Depending on the nature of the molecule, different absorption patterns allow molecules to be identified, but vibrational spectroscopy has much more to offer. The vibrational motions of the atoms a molecule induced by the light source conceal information on molecular structure and bonding. Professor Kraka and her team are developing and applying special software to untangle these complex motions utilizing SMU’s high-performance computer to uncover how the atoms in a molecule are connected and interact. Detailed knowledge about these interactions is expected to lead to progress in the field, ranging from fine-tuning and designing of new materials to understanding and modifying the biological activity in enzymes. The students engaged in this research project are gaining valuable experience in both cutting-edge modern computational spectroscopy and the use of a supercomputer as a powerful resource to help solving pending chemical problems, preparing them for a future career in a science, technology, engineering, and mathematics (STEM) field. Information on the electronic structure of a molecule, the strength of its bonds, its geometry, and its conformational flexibility is encoded in the vibrational motions of a molecule induced by IR light. However, these so-called normal vibrational modes are generally delocalized over the molecule caused by a coupling of the atomic movements during the vibration, which hinders the direct access to this valuable information. Local Vibrational Mode Analysis (LMA) being conducted by Professor Kraka and her team provides a unique solution to this problem by extracting local vibrational modes and related local properties, e.g., local mode force constants related to the intrinsic bond strengths for single molecules in the gas phase as well as for periodic systems. Local and normal vibrational modes are uniquely connected--the physical foundation of LMA--allowing for a unique decomposition of normal modes into local mode contributions. Specific applications of this approach include the exploration of metal-ligand bonding in a range of molecular settings from heavy-metal materials such as uranium compounds, to heme proteins of importance in biology. Topics in periodic systems to be studied include (i) the investigation of the complex bonding network in ice structures, (ii) a systematic study of bonding in ionic crystals and (iii) the development of a protocol for identifying salts and co-crystals. Broader impacts of this project include the release of a general-purpose open source LMA software package via the Github development platform to be shared with the spectroscopic community, the promotion of fruitful interactions between experimental and computational chemists working in the field of spectroscopy, and outreach to students from underserved populations.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.

在这个由化学部门化学结构动力学和机理- a （CSDM-A）计划资助的项目中，南卫理公会大学（SMU）的Elfi Kraka教授和她的计算和理论化学小组（CATCO）将使用振动光谱数据来获得关于分子的新见解。在过去的几十年里，振动光谱学已经发展成为一种重要的分析工具，在化学合成、生物分析、材料质量控制、法医科学或卫生部门有着广泛的应用。红外线（IR）具有激发分子振动的适当能量。根据分子的性质，不同的吸收模式允许分子被识别，但振动光谱学有更多的提供。由光源引起的原子和分子的振动运动掩盖了分子结构和键合的信息。Kraka教授和她的团队正在开发和应用特殊的软件来解开这些复杂的运动，利用SMU的高性能计算机来揭示分子中的原子是如何连接和相互作用的。对这些相互作用的详细了解有望导致该领域的进展，从微调和设计新材料到理解和修改酶的生物活性。参与该研究项目的学生在尖端的现代计算光谱学和使用超级计算机作为强大资源来帮助解决悬而未决的化学问题方面获得了宝贵的经验，为他们未来在科学、技术、工程和数学（STEM）领域的职业生涯做好了准备。分子的电子结构、化学键的强度、几何形状和构象柔韧性等信息都编码在红外光诱导下分子的振动运动中。然而，这些所谓的正常振动模式通常是由振动期间原子运动的耦合引起的分子上的离域，这阻碍了直接获取这些有价值的信息。Kraka教授和她的团队进行的局部振动模式分析（LMA）为这个问题提供了一个独特的解决方案，通过提取局部振动模式和相关的局部性质，例如，与气相单个分子和周期系统的固有键强度相关的局部模式力常数。局部和正常振动模态是唯一连接的- LMA的物理基础-允许将正常模态分解为局部模态贡献。这种方法的具体应用包括探索金属-配体在一系列分子设置中的结合，从重金属材料（如铀化合物）到生物学中重要的血红素蛋白。周期系统中要研究的主题包括(i)冰结构中复杂键合网络的研究，（ii）离子晶体中键合的系统研究，以及（iii）识别盐和共晶体的协议的发展。该项目的更广泛影响包括通过Github开发平台发布通用开源LMA软件包，与光谱社区共享，促进在光谱领域工作的实验和计算化学家之间富有成效的互动，以及向服务不足人群的学生提供服务。该奖项反映了美国国家科学基金会的法定使命，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。

项目成果

On the formation of CN bonds in Titan’s atmosphere—a unified reaction valley approach study

• DOI: 10.1007/s00894-021-04917-8
• 发表时间: 2021-10
• 期刊: Journal of Molecular Modeling
• 影响因子: 2.2
• 作者: M. Freindorf;Nassim Beiranvand;A. A. A. Delgado-A.-A.;Yunwen Tao;E. Kraka

Featuring a new computational protocol for the estimation of intensity and overall quantum yield in lanthanide chelates with applications to Eu(III) mercapto-triazole Schiff base ligands

• DOI: 10.1016/j.omx.2022.100216
• 发表时间: 2022-11
• 期刊: Optical Materials: X
• 作者: Renaldo T. Moura Jr.;Mateus M. Quintano;Carlos V. Santos-Jr.;Vinícius A.C.A. Albuquerque;E. C. Aguiar

Mechanistic Details of the Sharpless Epoxidation of Allylic Alcohols—A Combined URVA and Local Mode Study

• DOI: 10.3390/catal12070789
• 发表时间: 2022-07
• 期刊: Catalysts
• 影响因子: 3.9
• 作者: M. Freindorf;E. Kraka

Weak and strong π interactions between two monomers—assessed with local vibrational mode theory

两个单体之间的弱和强α相互作用——用局部振动模式理论进行评估

• DOI: 10.1139/cjc-2022-0254
• 发表时间: 2023
• 期刊: Canadian Journal of Chemistry
• 影响因子: 1.1
• 作者: Zou, Wenli;Freindorf, Marek;Oliveira, Vytor;Tao, Yunwen;Kraka, Elfi
• 通讯作者: Kraka, Elfi

The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena

• DOI: 10.1021/acs.jpca.2c05962
• 发表时间: 2022-11-08
• 期刊: JOURNAL OF PHYSICAL CHEMISTRY A
• 影响因子: 2.9
• 作者: Kraka，Elfi;Quintano，Mateus;Freindorf，Marek
• 通讯作者: Freindorf，Marek