溶液中的生物分子的形态能量:将MPCONF196基准扩展到显式水分子
Christoph Plett1, Stefan Grimme1, Andreas Hansen1
1Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany.
Journal of computational chemistry
|November 20, 2023
概括
准确预测生物分子构造能量的需要考虑溶剂效应. 一个新的基准集,solvMPCONF196,有明确的水分子,有助于开发可靠的计算方法,这些关键的相互作用.
科学领域:
- 计算化学的计算化学
- 分子建模分子建模
- 生物物理学的生物物理.
背景情况:
- 精确的分子性质的计算预测,如生物分子的结构能量,是必不可少的.
- 现有的基准集经常忽视溶剂相互作用,尽管生物分子通常存在于水溶液中.
- 这种局限性阻碍了对生物系统的强大可靠计算方法的开发.
研究的目的:
- 引入一个新的基准集,solvMPCONF196,其中包括明确的水分子来解释溶解效应.
- 为溶液中和宏循环的构造能提供高度准确的参考值.
- 评估各种计算方法的性能,以预测这些依赖于溶解的能量.
主要方法:
- 创建了solvMPCONF196基准,通过将气相MPCONF196组与明确的水分子进行溶解来设置.
- 使用PNO-LCCSD-F12b/AVQZ'方法计算非常准确的参考形态能量.
- 评估各种密度函数理论 (DFT) 函数,复合 DFT 方法,半经验方法和分子力学力场.
主要成果:
- 双混合功能revDSDPBEP86-D4/def2-QZVPP表现最好,实现了接近合集群质量的结构能量.
- 几种 (元) GGA和混合函数,包括B97M-V和B97M-D,具有很大的基准集,重现了基准值,平均绝对偏差 (MAD) 低于1kcal/mol.
- 复合DFT方法r2SCAN-3c提供了良好的效率和准确性的平衡 (MAD为1.2 kcal/mol).
结论:
- solvMPCONF196基准集有效地解决了评估方法的需要,这些方法包括溶剂效应在结构能量计算中.
- 对于像多和宏循环这样的大型系统,建议使用半实证的GFN2-xTB或MMFF94力场来提高计算效率.
- 这项研究为选择适合在水环境中进行生物分子模拟的计算方法提供了有价值的见解.
关键词:
一个基准的基准指标.形态能量是形态的能量.非共价相互作用非共价相互作用solvMPCONF196196F1966F1966F1966F1966F solvMPCONF1966F1966F1966F1966F1966F1966F solvMPCONF1966F1966F1966F1966F1966F1966F1966F1966F1966F solvMPCONF1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F1966F196F196F196F196F196F196F196F196F196F196F196F解决方法 解决方法更多相关视频
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