Statistical Mechanics with Quantum Potentials: Application to Host-Gues

具有量子势的统计力学：在主人-客人中的应用

• 批准号: 9248382
• 负责人: Simon Webb
• 金额: $ 73.47万
• 依托单位: VERACHEM, LLC
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2019-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9248382
• 关键词: Affect; Affinity; Algorithms; Applied Research; Area; Basic Science; Behavior; Binding; Binding Sites; Blinded; Cereals; Chemical Warfare Agents; Chemicals; Code; Computer software; Computing Methodologies; Coupled; Cyclodextrins; Data; Dissociation; Entropy; Excision; Flurbiprofen; Free Energy; Geometry; Goals; Health; Human; Hybrids; Industrialization; Investigation; Kinetics; Libraries; Link; Mechanics; Methodology; Methods; Molecular; Molecular Conformation; Movement; Pathologic; Pharmaceutical Preparations; Pharmacologic Substance; Phase; Potential Energy; Procedures; Process; Property; Quantum Mechanics; Research Personnel; Running; Scheme; Science; Scientist; Services; Small Business Innovation Research Grant; Software Tools; Speed; Statistical Mechanics; Technology; Testing; Thermodynamics; Time; Translating; base; beta-Cyclodextrins; blind; computerized tools; conformer; design; drug candidate; drug discovery; environmental chemical; experimental study; improved; molecular mechanics; parallel processing; physical property; pollutant; public health relevance; quantum; quantum chemistry; research and development; tool; vibration

DESCRIPTION (provided by applicant): Host molecules, such as cyclodextrins and cucurbiturils, can 'capture' smaller molecules and affect their physical and chemical behavior. The stronger the host molecule holds onto, i.e. binds, its smaller 'guest' the larger the effect ca be. Host molecules themselves can also be chemically altered (i.e. derivatized), which can change how strongly they bind guest molecules, as well as their own physical properties. Scientists are discovering many human health-related applications for host-guest technology, including improvement of the properties of drugs to make them more effective and safer, potential scavengers for chemical warfare agent removal, and clean-up of environmental chemical pollutants. The amount of basic research as well as applied/industrial R&D in this area is expanding rapidly. Given a particular 'guest' molecule (e.g. drug candidate, chemical pollutant) key pieces of information R&D scientists require is the host-guest binding affinity and the association/dissociation rates. This SBIR project aims to develop a software tool that can accurately predict these host-guest binding properties (e.g. binding free energy). This would allow R&D scientists to carry out computational experiments reducing the number of expensive and time-consuming bench experiments required. There is a current need for such a software tool to be developed, because as recently demonstrated by a blinded test challenge, existing tools are not accurate enough to provide useful information to researchers. Very recent studies indicate that the accuracy of the predictions can be significantly improved by combining quantum mechanical (QM) energy functions with rigorous statistical mechanics. However, these proof-of-concept studies have yet to be translated into a robust computational tool suitable for applied R&D. Therefore, this project will interface VeraChem's current statistical mechanics software package (VM2) with the widely used quantum chemistry package GAMESS, and implement drivers for various computational schemes to achieve this goal. In this proposed hybrid methodology, a Boltzmann distribution of molecular conformations will still be generated via a thorough conformational search as it is for classical VM2; however, the conformational search will not solely rely on molecular mechanics but will be guided by the more reliable QM potential. QM potentials will also be used for entropy terms, including a treatment of anharmonic effects. Full advantage will be taken of recent dramatic improvements in reliability of semi-empirical QM (SEQM), with optional corrections at higher levels of QM. Turnaround of calculations will be speeded up by parallel processing and a sophisticated conformer filter/vetting process.

描述(申请人提供)：宿主分子，如环糊精和瓜环，可以‘捕获’较小的分子，并影响它们的物理和化学行为。宿主分子与其较小的“客体”结合得越强，其影响就越大。主体分子本身也可以被化学改变(即衍生)，这可以改变它们与客体分子结合的强度，以及它们自己的物理性质。科学家们正在发现许多与人类健康相关的主客体技术应用，包括改善药物的性质以使其更有效和更安全，潜在的清除化学战剂的清道夫，以及清除环境化学污染物。这一领域的基础研究和应用/工业研发的数量正在迅速扩大。给定特定的“客体”分子(如候选药物、化学污染物)，研发科学家需要的关键信息是主-客体结合亲和力和缔合/解离速率。这个SBIR项目旨在开发一种软件工具，可以准确地预测这些主-客体结合属性(例如结合自由能)。这将允许研发科学家进行计算实验，减少所需的昂贵和耗时的台式实验的数量。目前需要开发这样的软件工具，因为正如最近的盲目测试挑战所表明的那样，现有的工具不够准确，不足以向研究人员提供有用的信息。最近的研究表明，通过将量子力学(QM)能量函数与严格的统计力学相结合，可以显著提高预测的准确性。然而，这些概念验证研究尚未转化为适用于应用研发的强大计算工具。因此，该项目将把VeraChem当前的统计力学软件包(VM2)与广泛使用的量子化学软件包GamesS相连接，并为各种计算方案实现驱动程序以实现这一目标。在这种提出的混合方法中，分子构象的玻尔兹曼分布仍然将通过彻底的构象搜索来产生，就像经典的VM2一样；然而，构象搜索将不会仅仅依赖于分子力学，而将由更可靠的QM势来指导。QM势也将用于熵项，包括非谐效应的处理。将充分利用最近半经验质量管理(SEQM)可靠性的显著提高，并在更高级别的质量管理中进行可选的修正。通过并行处理和复杂的构象过滤/审查过程，将加快计算的周转。

项目成果

Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm.

使用基于新量子力学的挖掘最小值算法计算主客体结合自由能。

• DOI: 10.1063/5.0040759
• 发表时间: 2021
• 期刊: The Journal of chemical physics
• 作者: Xu,Peng;Sattasathuchana,Tosaporn;Guidez,Emilie;Webb,SimonP;Montgomery,Kilinoelani;Yasini,Hussna;Pedreira,IaraFM;Gordon,MarkS
• 通讯作者: Gordon,MarkS