• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

用于NDDO衍生半经验模型的几何校正二次优化算法

Geometry-Corrected Quadratic Optimization Algorithm for NDDO-Descendant Semiempirical Models.

作者信息

Ong Adrian Wee Wen, Cao Steve Yueran, Chan Leemen Chee Yong, Lim Javier, Kwek Leong Chuan

机构信息

Centre for Quantum Technologies, National University of Singapore, Singapore 117543, Singapore.

MajuLab, CNRS-UNS-NUS-NTU International Joint Research Unit, UMI 3654, Singapore 117543, Singapore.

出版信息

J Chem Theory Comput. 2025 Jan 14;21(1):138-154. doi: 10.1021/acs.jctc.4c01070. Epub 2024 Dec 18.

DOI:10.1021/acs.jctc.4c01070
PMID:39694476
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11736688/
Abstract

The long-held assumption that the optimization of parameters for NDDO-descendant semiempirical methods may be performed without precise geometry optimization is assessed in detail; the relevant equations for the analytical evaluation of the geometry-corrected derivatives of molecular properties that account for changes in the optimum geometry are then presented. The first and second derivatives calculated from our implementation of MNDO are used for a limited reparameterization of 1,113 CHNO molecules taken from the PM7 training set, demonstrating an improvement over the PARAM program used in the optimization of parameters for the PMx methods.

摘要

长期以来一直认为,在不进行精确几何优化的情况下就可以对NDDO衍生的半经验方法的参数进行优化,本文对此进行了详细评估;随后给出了用于分析评估分子性质的几何校正导数的相关方程,这些导数考虑了最佳几何结构的变化。从我们实现的MNDO计算得到的一阶和二阶导数,被用于对从PM7训练集中选取的1113个CHNO分子进行有限的重新参数化,结果表明相较于用于PMx方法参数优化的PARAM程序有了改进。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/b1aad652716c/ct4c01070_0017.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/442744744ac4/ct4c01070_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/9d80afac22c4/ct4c01070_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/84a125900bcc/ct4c01070_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/e99136210d66/ct4c01070_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/594ab57bf541/ct4c01070_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/ca48cad92f91/ct4c01070_0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/043bc7d7dbda/ct4c01070_0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/ceddc53ffc8e/ct4c01070_0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/980acbc48b83/ct4c01070_0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/1c422412a4d1/ct4c01070_0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/70e3c2f913d6/ct4c01070_0011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/f61a57bd694a/ct4c01070_0012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/2368141f2f69/ct4c01070_0013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/04f7d9ef81fc/ct4c01070_0014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/516989f38bbc/ct4c01070_0015.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/776b40ffd5c1/ct4c01070_0016.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/b1aad652716c/ct4c01070_0017.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/442744744ac4/ct4c01070_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/9d80afac22c4/ct4c01070_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/84a125900bcc/ct4c01070_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/e99136210d66/ct4c01070_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/594ab57bf541/ct4c01070_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/ca48cad92f91/ct4c01070_0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/043bc7d7dbda/ct4c01070_0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/ceddc53ffc8e/ct4c01070_0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/980acbc48b83/ct4c01070_0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/1c422412a4d1/ct4c01070_0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/70e3c2f913d6/ct4c01070_0011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/f61a57bd694a/ct4c01070_0012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/2368141f2f69/ct4c01070_0013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/04f7d9ef81fc/ct4c01070_0014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/516989f38bbc/ct4c01070_0015.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/776b40ffd5c1/ct4c01070_0016.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6100/11736688/b1aad652716c/ct4c01070_0017.jpg

相似文献

1
Geometry-Corrected Quadratic Optimization Algorithm for NDDO-Descendant Semiempirical Models.用于NDDO衍生半经验模型的几何校正二次优化算法
J Chem Theory Comput. 2025 Jan 14;21(1):138-154. doi: 10.1021/acs.jctc.4c01070. Epub 2024 Dec 18.
2
An improved parameterization procedure for NDDO-descendant semi-empirical methods.一种改进的 NDDO 衍生物半经验方法的参数化程序。
J Mol Model. 2023 Mar 28;29(4):118. doi: 10.1007/s00894-023-05499-3.
3
Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters.半经验方法参数优化 VI:对 NDDO 近似的更多修正和参数的重新优化。
J Mol Model. 2013 Jan;19(1):1-32. doi: 10.1007/s00894-012-1667-x. Epub 2012 Nov 28.
4
Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties.半经验量子化学正交化校正方法:基态性质的基准
J Chem Theory Comput. 2016 Mar 8;12(3):1097-120. doi: 10.1021/acs.jctc.5b01047. Epub 2016 Jan 29.
5
Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens.将PDDG/PM3和PDDG/MNDO半经验分子轨道方法扩展至卤素。
J Comput Chem. 2004 Jan 15;25(1):138-50. doi: 10.1002/jcc.10356.
6
NO-MNDO:  Reintroduction of the Overlap Matrix into MNDO.NO-MNDO:将重叠矩阵重新引入MNDO。
J Chem Theory Comput. 2006 Mar;2(2):413-9. doi: 10.1021/ct050174c.
7
Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements.半经验方法参数的优化IV:将MNDO、AM1和PM3扩展到更多主族元素。
J Mol Model. 2004 Apr;10(2):155-64. doi: 10.1007/s00894-004-0183-z. Epub 2004 Mar 2.
8
PDDG/PM3 and PDDG/MNDO: improved semiempirical methods.PDDG/PM3和PDDG/MNDO:改进的半经验方法。
J Comput Chem. 2002 Dec;23(16):1601-22. doi: 10.1002/jcc.10162.
9
An optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework.半经验分子轨道法在溶液化学中的最优策略。II. 在QM/MM 框架中重现静电相互作用的首要重要性。
J Comput Chem. 2010 Nov 15;31(14):2628-41. doi: 10.1002/jcc.21558.
10
Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements.半经验方法参数的优化V:NDDO近似的修正及对70种元素的应用
J Mol Model. 2007 Dec;13(12):1173-213. doi: 10.1007/s00894-007-0233-4. Epub 2007 Sep 9.

本文引用的文献

1
Nuclear Quantum Effects on Nonadiabatic Dynamics of a Green Fluorescent Protein Chromophore Analogue: Ring-Polymer Surface-Hopping Simulation.核量子效应在绿色荧光蛋白发色团类似物非绝热动力学中的作用:环聚合物表面跳跃模拟
J Chem Theory Comput. 2024 May 14;20(9):3426-3439. doi: 10.1021/acs.jctc.4c00068. Epub 2024 Apr 24.
2
A semiempirical method optimized for modeling proteins.一种用于蛋白质建模的半经验方法。
J Mol Model. 2023 Aug 22;29(9):284. doi: 10.1007/s00894-023-05695-1.
3
An improved parameterization procedure for NDDO-descendant semi-empirical methods.
一种改进的 NDDO 衍生物半经验方法的参数化程序。
J Mol Model. 2023 Mar 28;29(4):118. doi: 10.1007/s00894-023-05499-3.
4
How well do semiempirical QM methods describe the structure of proteins?半经验量子力学方法对蛋白质结构的描述有多准确?
J Chem Phys. 2023 Jan 28;158(4):044118. doi: 10.1063/5.0135091.
5
Machine learning and semi-empirical calculations: a synergistic approach to rapid, accurate, and mechanism-based reaction barrier prediction.机器学习与半经验计算:一种用于快速、准确且基于机理的反应势垒预测的协同方法。
Chem Sci. 2022 Jun 14;13(25):7594-7603. doi: 10.1039/d2sc02925a. eCollection 2022 Jun 29.
6
A Computational Study of the Promiscuity of the SAM-Dependent Methyltransferase AtHTMT1.对依赖S-腺苷甲硫氨酸的甲基转移酶AtHTMT1的混杂性的计算研究
ACS Omega. 2022 Apr 6;7(15):12753-12764. doi: 10.1021/acsomega.1c07327. eCollection 2022 Apr 19.
7
Discovery of RTA ricin subunit inhibitors: a computational study using PM7 quantum chemical method and steered molecular dynamics.RTA 蓖麻毒素亚基抑制剂的发现:使用 PM7 量子化学方法和导向分子动力学的计算研究。
J Biomol Struct Dyn. 2022 Aug;40(12):5427-5445. doi: 10.1080/07391102.2021.1878058. Epub 2021 Feb 2.
8
Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties.半经验量子化学正交化校正方法:基态性质的基准
J Chem Theory Comput. 2016 Mar 8;12(3):1097-120. doi: 10.1021/acs.jctc.5b01047. Epub 2016 Jan 29.
9
NO-MNDO:  Reintroduction of the Overlap Matrix into MNDO.NO-MNDO:将重叠矩阵重新引入MNDO。
J Chem Theory Comput. 2006 Mar;2(2):413-9. doi: 10.1021/ct050174c.
10
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods.半经验量子力学方法中氢键和色散作用的高级校正
J Chem Theory Comput. 2012 Jan 10;8(1):141-51. doi: 10.1021/ct200751e. Epub 2011 Dec 22.