From Theory of Energy Decomposition Analysis to Rational Force Field Design

从能量分解分析理论到合理力场设计

基本信息

  • 批准号:
    1665315
  • 负责人:
  • 金额:
    $ 66万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Continuing Grant
  • 财政年份:
    2017
  • 资助国家:
    美国
  • 起止时间:
    2017-08-01 至 2020-07-31
  • 项目状态:
    已结题

项目摘要

Teresa Head-Gordon and Martin Head-Gordon are supported by an award from the Chemical Theory, Models and Computational Methods program in the Division of Chemistry to develop computational and theoretical models and methods that can be used to make accurate predictions for the behavior of complex molecular and bimolecular systems. This collaborative project combines the mutual development of advanced force fields and energy decomposition analysis (EDA). The field of biomolecular modeling and simulation currently relies on a simple representation of the potential energy surface of molecules based on what is known as the "pairwise additive" force field. But to design new drugs or new biomaterials the field needs new and higher accuracy molecular mechanics (MM) force fields. These new force fields introduce new terms that describe processes not considered in simple pair-wise force fields, for example, polarization and charge transfer. The introduction of such terms pose great challenges for rational force field design as well algorithmic and software challenges. The force field development is enabled in part by using information from an energy decomposition method (EDA) that is based on state-of-the art quantum mechanical (QM) calculations. This collaborative proposal is a partnership that couple's advances in EDA methods with the design and validation of next generation force fields, in a way that permits each to advance the impact of the other. These methods are used to help synthetic chemists make new drugs, to aid in the design of new functional materials, and to create new catalysts that speed up chemical reactions by many orders of magnitude. All the methods developments resulting from this proposal are being implemented in many widely used computational chemistry software packages. The proposed research is built on three main thrusts. First, to impact the efficiency of polarizable force fields, a new procedure to avoid self-consistent iterations is being developed for use in MM dynamics, and within the inner loop of QM/MM calculations. Second, the two research groups are engaged in a major effort to test and improve MM parameters in polarizable force fields for condensed phase modeling, to assess non-bonded parameters for Pauli-exclusion, permanent electrostatics, polarization, and to explore models for additional short-range contributions from charge penetration, charge transfer, and exchange repulsion. In addition, attention is paid to torsional and solute-solvent interactions in biomolecules, where there is significant scope for improvement. These efforts, informed by EDA tools, are complemented by validation studies including scalar couplings in polypeptides, Stark effects and melting curves in three proteins. Specific outcomes include an upgraded polarizable potential of the AMOEBA family, as a well as more advanced model that includes additional non-classical terms. The third thrust is the development of EDA methods. New capabilities that inform the MM developments include force decomposition analysis, partitioning of polarization into direct and indirect terms and the many-body decomposition of the latter. A soundly based EDA for coupled cluster (CC) theory is being developed. Finally, new advances in variational EDA for chemical bonds are pioneered including multiple bonds and dynamical correlation. When developed the advanced MM potential energy surfaces methodology and models will be provided to OpenMM, OMNIA, TINKER, and LibEFP, and the new proposed EDA capabilities to Q-Chem and ONETEP. The Head-Gordon groups develop training materials based on this research for use in computational chemistry community workshops and schools. Plans are to distribute these materials through interaction with the Molecular Sciences Software Institute (MolSSI) as well as through Q-Chem's instructional support web pages
Teresa Head-Gordon和Martin Head-Gordon获得了化学学部化学理论、模型和计算方法项目的奖励,他们开发了计算和理论模型和方法,可用于准确预测复杂分子和双分子系统的行为。这个合作项目结合了先进力场和能量分解分析(EDA)的相互发展。生物分子建模和模拟领域目前依赖于基于所谓的“成对相加”力场的分子势能表面的简单表示。但为了设计新的药物或新的生物材料,该领域需要新的和更高精度的分子力学力场。这些新的力场引入了新的术语来描述在简单的成对力场中没有考虑到的过程,例如,极化和电荷转移。这些术语的引入对理性力场设计以及算法和软件的挑战提出了巨大的挑战。力场的开发部分是通过使用基于最先进的量子力学(QM)计算的能量分解方法(EDA)的信息实现的。这项合作提案是一种伙伴关系,将EDA方法的进步与下一代力场的设计和验证结合起来,以一种允许彼此推进对方影响的方式。这些方法被用来帮助合成化学家制造新药,帮助设计新的功能材料,并创造新的催化剂,使化学反应速度提高许多个数量级。所有的方法发展产生了这一建议是在许多广泛使用的计算化学软件包实现。拟议的研究建立在三个主要方面。首先,为了影响极化力场的效率,正在开发一种新的程序来避免自一致迭代,用于MM动力学,以及在QM/MM计算的内环中。其次,这两个研究小组正致力于测试和改进用于凝聚相建模的极化力场中的MM参数,以评估泡利不相容、永久静电、极化的非键参数,并探索电荷穿透、电荷转移和交换排斥等其他短程贡献的模型。此外,还关注生物分子中的扭转和溶质-溶剂相互作用,这方面还有很大的改进空间。这些努力,由EDA工具提供信息,由验证研究补充,包括多肽的标量偶联、斯塔克效应和三种蛋白质的熔化曲线。具体结果包括变形虫家族极化电位的升级,以及包含额外非经典项的更先进的模型。第三个推动力是EDA方法的发展。为MM开发提供信息的新功能包括力分解分析、将极化划分为直接项和间接项以及后者的多体分解。一个基于完善的耦合簇(CC)理论EDA正在被开发。最后,介绍了化学键变分EDA的新进展,包括多键和动态相关。开发出先进的MM势能面方法和模型后,将提供给OpenMM、OMNIA、TINKER和LibEFP,并向Q-Chem和ONETEP提供新的EDA功能。Head-Gordon小组根据这项研究开发了用于计算化学社区研讨会和学校的培训材料。计划通过与分子科学软件研究所(MolSSI)的互动以及Q-Chem的教学支持网页来分发这些材料

项目成果

期刊论文数量(28)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Systematic Optimization of Water Models Using Liquid/Vapor Surface Tension Data
  • DOI:
    10.1021/acs.jpcb.9b05455
  • 发表时间:
    2019-08-15
  • 期刊:
  • 影响因子:
    3.3
  • 作者:
    Qiu, Yudong;Nerenberg, Paul S.;Wang, Lee-Ping
  • 通讯作者:
    Wang, Lee-Ping
Compressed representation of dispersion interactions and long-range electronic correlations
色散相互作用和远程电子关联的压缩表示
  • DOI:
    10.1063/1.4997186
  • 发表时间:
    2017
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Gonthier, Jérôme F.;Head-Gordon, Martin
  • 通讯作者:
    Head-Gordon, Martin
On the Computational Characterization of Charge-Transfer Effects in Noncovalently Bound Molecular Complexes
  • DOI:
    10.1021/acs.jctc.7b01256
  • 发表时间:
    2018-05-01
  • 期刊:
  • 影响因子:
    5.5
  • 作者:
    Mao, Yuezhi;Ge, Qinghui;Head-Gordon, Martin
  • 通讯作者:
    Head-Gordon, Martin
Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration
将无迭代偏振与大时间步随机等速积分相结合
  • DOI:
    10.1021/acs.jctc.9b00072
  • 发表时间:
    2019
  • 期刊:
  • 影响因子:
    5.5
  • 作者:
    Albaugh, Alex;Tuckerman, Mark E.;Head-Gordon, Teresa
  • 通讯作者:
    Head-Gordon, Teresa
A New Method for Treating Drude Polarization in Classical Molecular Simulation
经典分子模拟中处理粗极化的新方法
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Teresa Head-Gordon其他文献

Amyloid-Beta Heterogeneous Conformational Ensembles: Differences Between the 40- and 42-Residue Peptides and Implications for Dimer Polyamorphism
  • DOI:
    10.1016/j.bpj.2011.11.3437
  • 发表时间:
    2012-01-31
  • 期刊:
  • 影响因子:
  • 作者:
    K. Aurelia Ball;Aaron H. Phillips;Nicolas L. Fawzi;David E. Wemmer;Teresa Head-Gordon
  • 通讯作者:
    Teresa Head-Gordon
The Combined Force Field-Sampling Problem in Simulation of Intrinsically Disordered Peptides
  • DOI:
    10.1016/j.bpj.2017.11.3641
  • 发表时间:
    2018-02-02
  • 期刊:
  • 影响因子:
  • 作者:
    James Lincoff;Sukanya Sasmal;Teresa Head-Gordon
  • 通讯作者:
    Teresa Head-Gordon
A Coarse Grained Molecular Dynamics Study of Amyloid Beta Transmembrane Pores
  • DOI:
    10.1016/j.bpj.2011.11.1331
  • 发表时间:
    2012-01-31
  • 期刊:
  • 影响因子:
  • 作者:
    Shachi Katira;Teresa Head-Gordon
  • 通讯作者:
    Teresa Head-Gordon
Biological insights from integrative modeling of intrinsically disordered protein systems
来自内在无序蛋白质系统综合建模的生物学见解
  • DOI:
    10.1016/j.sbi.2025.103063
  • 发表时间:
    2025-08-01
  • 期刊:
  • 影响因子:
    7.000
  • 作者:
    Zi Hao Liu;Maria Tsanai;Oufan Zhang;Teresa Head-Gordon;Julie D. Forman-Kay
  • 通讯作者:
    Julie D. Forman-Kay
Evaluation and Improvement of the Amber ff99SB Force Field with an Advanced Water Model
  • DOI:
    10.1016/j.bpj.2010.12.1900
  • 发表时间:
    2011-02-02
  • 期刊:
  • 影响因子:
  • 作者:
    Paul S. Nerenberg;Clare So;Ajay Tripathy;Teresa Head-Gordon
  • 通讯作者:
    Teresa Head-Gordon

Teresa Head-Gordon的其他文献

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{{ truncateString('Teresa Head-Gordon', 18)}}的其他基金

Reactive Force Field Design Guided by Energy Decomposition Analysis
能量分解分析引导的反作用力场设计
  • 批准号:
    2313791
  • 财政年份:
    2023
  • 资助金额:
    $ 66万
  • 项目类别:
    Continuing Grant
Reactive and Non-Reactive Force Field Design Guided by Advances in Energy Decomposition Analysis
以能量分解分析进展为指导的反应性和非反应性力场设计
  • 批准号:
    1955643
  • 财政年份:
    2020
  • 资助金额:
    $ 66万
  • 项目类别:
    Continuing Grant
Collaborative Research: S2I2: Conceptualization of a Center for Biomolecular Simulation
合作研究:S2I2:生物分子模拟中心的概念化
  • 批准号:
    1331445
  • 财政年份:
    2014
  • 资助金额:
    $ 66万
  • 项目类别:
    Standard Grant
Many-Body Expansion of Direct and Mutual Polarization Models
直接极化和互极化模型的多体扩展
  • 批准号:
    1363320
  • 财政年份:
    2014
  • 资助金额:
    $ 66万
  • 项目类别:
    Continuing Grant
Collaborative Research: SI2-CHE: Development and Deployment of Chemical Software for Advanced Potential Energy Surfaces
合作研究:SI2-CHE:先进势能表面化学软件的开发和部署
  • 批准号:
    1265731
  • 财政年份:
    2013
  • 资助金额:
    $ 66万
  • 项目类别:
    Standard Grant
Conference: Undergraduate Opportunities at the UC System Wide Bioengineering Symposium, June 21 - June 23, 2012, Berkeley, CA
会议:加州大学系统生物工程研讨会本科生机会,2012 年 6 月 21 日至 6 月 23 日,加利福尼亚州伯克利
  • 批准号:
    1243416
  • 财政年份:
    2012
  • 资助金额:
    $ 66万
  • 项目类别:
    Standard Grant
Potential Energy Surfaces of Various Accuracy for Biomolecular Simulations
用于生物分子模拟的各种精度的势能面
  • 批准号:
    1147444
  • 财政年份:
    2011
  • 资助金额:
    $ 66万
  • 项目类别:
    Standard Grant
Collaborative Research: Cyberinfrastructure for Next Generation Biomolecular Modeling
合作研究:下一代生物分子建模的网络基础设施
  • 批准号:
    0535710
  • 财政年份:
    2005
  • 资助金额:
    $ 66万
  • 项目类别:
    Continuing Grant

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Reactive Force Field Design Guided by Energy Decomposition Analysis
能量分解分析引导的反作用力场设计
  • 批准号:
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  • 财政年份:
    2023
  • 资助金额:
    $ 66万
  • 项目类别:
    Continuing Grant
Rigorous decomposition methods for planning and scheduling of energy networks
能源网络规划和调度的严格分解方法
  • 批准号:
    RGPIN-2019-05217
  • 财政年份:
    2022
  • 资助金额:
    $ 66万
  • 项目类别:
    Discovery Grants Program - Individual
Catalytic Ammonia Decomposition in Green Energy Supply
绿色能源供应中的催化氨分解
  • 批准号:
    2754045
  • 财政年份:
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Rigorous decomposition methods for planning and scheduling of energy networks
能源网络规划和调度的严格分解方法
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Reactive and Non-Reactive Force Field Design Guided by Advances in Energy Decomposition Analysis
以能量分解分析进展为指导的反应性和非反应性力场设计
  • 批准号:
    1955643
  • 财政年份:
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    $ 66万
  • 项目类别:
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能源网络规划和调度的严格分解方法
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    RGPIN-2019-05217
  • 财政年份:
    2019
  • 资助金额:
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随机波和涡流:流动分解和能量通量
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Energy Exchange Mechanism on the Turbulent and non-turbulent Interface by means of Intermediate Mean Kinematic Energy Based on 5-component Decomposition
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