Density Functional Theory for van der Waals Interactions

范德华相互作用的密度泛函理论

• 批准号: 8138333
• 负责人: JING KONG
• 金额: $ 21.24万
• 依托单位: Q-CHEM, INC.
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-01 至 2013-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8138333
• 关键词: Accounting; Alkanes; Behavior; Binding; Biological; Biological Models; Biology; Carbohydrates; Chemistry; Cisplatin; DNA; Development; Dipeptides; Discipline; Electronics; Evaluation; Failure; Feasibility Studies; Goals; Lead; Methods; Modeling; Molecular; Molecular Biology; Molecular Conformation; Molecular Models; Names; Nuclear; Phase; Photoreceptors; Play; Process; Proteins; Relative (related person); Reporting; Research Personnel; Role; Science; Series; Signal Transduction; Solutions; System; Techniques; Testing; Theoretical model; Time; Variant; Work; approach behavior; base; biological research; biological systems; chemical property; chemotherapy; cost; density; design; dipole moment; drug discovery; improved; interest; molecular modeling; molecular recognition; programs; public health relevance; quantum chemistry; research and development; theories

DESCRIPTION (provided by applicant): Q-Chem is a state-of-the-art commercial quantum chemistry program that is used to model atomic and molecular processes over a wide range of disciplines, including biology, chemistry, and materials science. Among the quantum chemistry methods, density functional theory (DFT) is perhaps the most widely used, especially in molecular biology, due to its ability to accurately model a wide range of molecular systems with reasonable computational cost. Despite its wide use, DFT does not include the dispersion correlation effect, or van der Waals interaction, which plays a critical role in the determination of the overall conformations of molecular systems and accordingly, is indispensable in the study of DNA and proteins, molecular recognition, the packing of crystals, etc. In Phase I of this project, we developed an efficient SCF and nuclear gradient solution for a density functional dispersion model called XDM, and demonstrated that it corrected some of the failures of current DFT methods in structural and energetic studies. In this Phase II proposal, we plan to incorporate dispersion of the XDM model into all the major aspects of DFT applications, including energetic and structural calculations of both ground and excited electronic states, with further improved accuracy. To demonstrate the utility of the DFT-XDM approach for modeling systems of biological interest, we will investigate two challenging molecular processes, namely the binding process of cisplatin to DNA, and electronic transitions in photoactive yellow protein (PYP). Cisplatin is widely used in chemotherapy, and photoactive yellow protein is a widely studied photoreceptor that is key to understanding signal transduction. As we will show, the successful development and implementation of the DFT-XDM model proposed here will lead to much more accurate DFT solutions. PUBLIC HEALTH RELEVANCE: This project aims to develop and implement a very accurate DFT method. DFT is at the core of molecular modeling and is applied widely in biological research/development and in drug discovery. The improved DFT will significantly increase researchers' quality of work and extend the application scope of DFT.

描述（由申请人提供）：Q Chem是一种最先进的商业量子化学计划，用于在广泛的学科上建模原子和分子过程，包括生物学，化学和材料科学。在量子化学方法中，密度功能理论（DFT）可能是最广泛使用的，尤其是在分子生物学中，因为它能够准确地对具有合理计算成本的广泛分子系统建模。尽管它广泛使用，但DFT并不包括分散相关效应，或者范德华（Van der Wa）的相互作用，在确定分子系统的整体构象中起着至关重要的作用，因此在DNA和蛋白质的研究中是必不可少的，在分子识别的研究中是必不可少的。证明它在结构和能量研究中纠正了当前DFT方法的某些失败。在此II阶段提案中，我们计划将XDM模型的分散纳入DFT应用的所有主要方面，包括地面和激发电子状态的能量和结构计算，并进一步提高精度。为了证明DFT-XDM方法对生物学意义的建模系统的实用性，我们将研究两个具有挑战性的分子过程，即顺铂与DNA的结合过程以及光活性黄蛋白（PYP）中的电子过渡。顺铂广泛用于化学疗法，光活性黄蛋白是一种广泛研究的光感受器，是理解信号转导的关键。正如我们将表明的那样，此处提出的DFT-XDM模型的成功开发和实施将导致更准确的DFT解决方案。 公共卫生相关性：该项目旨在开发和实施一种非常准确的DFT方法。 DFT是分子建模的核心，广泛应用于生物学研究/发育和药物发现。改进的DFT将大大提高研究人员的工作质量并扩大DFT的应用范围。