Automated high-throughput organic crystal structure prediction via population-based sampling

被引:0
|
作者
Zhu, Qiang [1 ]
Hattori, Shinnosuke [2 ]
机构
[1] Univ North Carolina Charlotte, Dept Mech Engn & Engn Sci, Charlotte, NC 28223 USA
[2] Sony Grp Corp, Adv Res Lab, Res Platform, 4-14-1 Asahi Cho, Atsugi 2430014, Japan
来源
DIGITAL DISCOVERY | 2025年 / 4卷 / 01期
关键词
EVOLUTIONARY ALGORITHM; MOLECULAR-CRYSTALS; BLIND TEST; POLYMORPHISM; LETHALITY; PROGRAM; ENERGY;
D O I
10.1039/d4dd00264d
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
With advancements in computational molecular modeling and powerful structure search methods, it is now possible to systematically screen crystal structures for small organic molecules. In this context, we introduce the Python package High-Throughput Organic Crystal Structure Prediction (HTOCSP), which enables the prediction and screening of crystal packing for small organic molecules in an automated, high-throughput manner. Specifically, we describe the workflow, which encompasses molecular analysis, force field generation, and crystal generation and sampling, all within customized constraints based on user input. We demonstrate the application of HTOCSP by systematically screening organic crystals for 100 molecules using different sampling strategies and force field options. Furthermore, we analyze the benchmark results to understand the underlying factors that may influence the complexity of the crystal energy landscape. Finally, we discuss the current limitations of the package and potential future extensions.
引用
收藏
页码:120 / 134
页数:15
相关论文
共 50 条
  • [1] Data Mining Approaches to High-Throughput Crystal Structure and Compound Prediction
    Hautier, Geoffroy
    PREDICTION AND CALCULATION OF CRYSTAL STRUCTURES: METHODS AND APPLICATIONS, 2014, 345 : 139 - 179
  • [2] High dielectric ternary oxides from crystal structure prediction and high-throughput screening
    Qu, Jingyu
    Zagaceta, David
    Zhang, Weiwei
    Zhu, Qiang
    SCIENTIFIC DATA, 2020, 7 (01)
  • [3] High dielectric ternary oxides from crystal structure prediction and high-throughput screening
    Jingyu Qu
    David Zagaceta
    Weiwei Zhang
    Qiang Zhu
    Scientific Data, 7
  • [4] In silico prediction and screening of modular crystal structures via a high-throughput genomic approach
    Yi Li
    Xu Li
    Jiancong Liu
    Fangzheng Duan
    Jihong Yu
    Nature Communications, 6
  • [5] In silico prediction and screening of modular crystal structures via a high-throughput genomic approach
    Li, Yi
    Li, Xu
    Liu, Jiancong
    Duan, Fangzheng
    Yu, Jihong
    NATURE COMMUNICATIONS, 2015, 6
  • [6] Quantitative High-Throughput Screening for Chemical Toxicity in a Population-Based In Vitro Model
    Lock, Eric F.
    Abdo, Nour
    Huang, Ruili
    Xia, Menghang
    Kosyk, Oksana
    O'Shea, Shannon H.
    Zhou, Yi-Hui
    Sedykh, Alexander
    Tropsha, Alexander
    Austin, Christopher P.
    Tice, Raymond R.
    Wright, Fred A.
    Rusyn, Ivan
    TOXICOLOGICAL SCIENCES, 2012, 126 (02) : 578 - 588
  • [7] High-throughput crystal structure solution using prototypes
    Griesemer, Sean D.
    Ward, Logan
    Wolverton, Chris
    PHYSICAL REVIEW MATERIALS, 2021, 5 (10)
  • [8] 24 hours - High-Throughput Crystal Structure Production
    Wagner, T.
    Kroemer, M.
    Grunwald, B.
    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2014, 70 : C695 - C695
  • [9] Motif based high-throughput structure prediction of superconducting monolayer titanium boride
    Yu, Ju-Song
    Liao, Ji-Hai
    Zhao, Yu-Jun
    Zhao, Yin-Chang
    Yang, Xiao-Bao
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2020, 22 (28) : 16236 - 16243
  • [10] Automated crystallographic system for high-throughput protein structure determination
    Brunzelle, JS
    Shafaee, P
    Yang, XJ
    Weigand, S
    Ren, Z
    Anderson, WF
    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2003, 59 : 1138 - 1144