• 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

采用分子力学和量子化学相结合的方法,对具有己基和庚基取代基的特罗格碱衍生物在溶液中的威尔科克斯扭力天平进行研究。

Study of the Wilcox torsion balance in solution for a Tröger's base derivative with hexyl-and heptyl substituents using a combined molecular mechanics and quantum chemistry approach.

作者信息

Heßelmann Andreas, Ferraro Federica

机构信息

Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, 91058, Erlangen, Germany.

出版信息

J Mol Model. 2019 Feb 18;25(3):69. doi: 10.1007/s00894-019-3935-5.

DOI:10.1007/s00894-019-3935-5
PMID:30778689
Abstract

The folding equilibrium of the Wilcox torsion balance in solution has been studied using a molecular mechanics method for sampling the conformational space and semi-empirical and density-functional quantum chemistry methods for characterizing the relative stabilities of various solute-solvent clusters extracted with the aid of the MD-quench technique from the different simulations that were performed. The role of the solvent environment has been analyzed by choosing four solvents of different polarities, namely water, acetone, tetrachloromethane, and n-hexane. In all cases, it is found that the attractive intramolecular interactions in folded conformations are strongly compensated by the increase of the solute-solvent interaction energies when the molecule unfolds. The latter can be well explained by the larger number of solvent molecules that can bind to the Wilcox molecule when in an unfolded conformation. The results of this work therefore support the experimental results of Yang et al. (Nature Chem 5:1006, 2013) that the folding free energy of the Wilcox balance is strongly reduced in solution as compared to the gas phase.

摘要

利用分子力学方法对溶液中威尔科克斯扭力天平的折叠平衡进行了研究,该方法用于采样构象空间,半经验和密度泛函量子化学方法用于表征借助MD淬火技术从不同模拟中提取的各种溶质 - 溶剂簇的相对稳定性。通过选择四种不同极性的溶剂,即水、丙酮、四氯化碳和正己烷,分析了溶剂环境的作用。在所有情况下,都发现当分子展开时,折叠构象中具有吸引力的分子内相互作用会被溶质 - 溶剂相互作用能的增加强烈补偿。后者可以很好地解释为当处于展开构象时,可以与威尔科克斯分子结合的溶剂分子数量更多。因此,这项工作的结果支持了Yang等人(《自然·化学》5:1006,2013)的实验结果,即与气相相比,威尔科克斯天平在溶液中的折叠自由能大大降低。

相似文献

1
Study of the Wilcox torsion balance in solution for a Tröger's base derivative with hexyl-and heptyl substituents using a combined molecular mechanics and quantum chemistry approach.采用分子力学和量子化学相结合的方法,对具有己基和庚基取代基的特罗格碱衍生物在溶液中的威尔科克斯扭力天平进行研究。
J Mol Model. 2019 Feb 18;25(3):69. doi: 10.1007/s00894-019-3935-5.
2
Theoretical studies of the Wilcox molecular torsion balance. Is the edge-to-face aromatic interaction important?
Org Lett. 1999 Dec 30;1(13):2049-51. doi: 10.1021/ol991019d.
3
Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations.由分子动力学模拟推导得出的溶剂对丙氨酸二肽构象行为的影响。
J Mol Graph Model. 2017 Nov;78:118-128. doi: 10.1016/j.jmgm.2017.10.005. Epub 2017 Oct 12.
4
Importance of polarization in quantum mechanics/molecular mechanics descriptions of electronic excited states: NaI(H2O)n photodissociation dynamics as a case study.极化在电子激发态的量子力学/分子力学描述中的重要性:以NaI(H₂O)ₙ光解离动力学为例进行研究
J Phys Chem B. 2008 Jan 17;112(2):636-49. doi: 10.1021/jp709656z.
5
Structures and properties of molecular torsion balances to decipher the nature of substituent effects on the aromatic edge-to-face interaction.分子扭转平衡的结构与性质,用于解读取代基对芳环边对面相互作用的影响本质。
Chemistry. 2014 Apr 14;20(16):4608-16. doi: 10.1002/chem.201304810. Epub 2014 Mar 20.
6
Theoretical study of the competition between intramolecular hydrogen bonds and solvation in the Cys-Asn-Ser tripeptide.Cys-Asn-Ser 三肽分子内氢键与溶剂化竞争的理论研究。
J Phys Chem B. 2010 Jul 15;114(27):8961-70. doi: 10.1021/jp1035162.
7
Molecular Dynamics and Free Energy Study of the Conformational Equilibria in the UUUU RNA Hairpin.UUUU RNA 发夹构象平衡的分子动力学和自由能研究。
J Chem Theory Comput. 2007 Jul;3(4):1435-50. doi: 10.1021/ct6003388.
8
Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.用于精确计算溶液和酶中反应能量学的量子力学/分子力学最小自由能路径:在平均力势面上的顺序采样与优化
J Chem Phys. 2008 Jan 21;128(3):034105. doi: 10.1063/1.2816557.
9
Adsorption behavior of the (+/-)-Tröger's base enantiomers in the phase system of a silica-based packing coated with amylose tri(3,5-dimethyl carbamate) and 2-propanol and molecular modeling interpretation.(±)-托品碱对映体在涂有直链淀粉三(3,5-二甲基氨基甲酸酯)的硅胶基质填料与2-丙醇的相体系中的吸附行为及分子模拟解释
J Chromatogr A. 2006 Apr 28;1113(1-2):148-61. doi: 10.1016/j.chroma.2006.02.001. Epub 2006 Mar 3.
10
Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.蛋白质天然构象与故意错误折叠构象之间的区分:ES/IS,一种计算构象自由能的新方法,该方法同时使用了含显式溶剂的动力学模拟和隐式溶剂连续介质模型。
Proteins. 1998 Sep 1;32(4):399-413.

引用本文的文献

1
Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide.水合壳对丙氨酸-亮氨酸-丙氨酸-亮氨酸肽中羰基振动的影响。
Molecules. 2021 Apr 8;26(8):2148. doi: 10.3390/molecules26082148.

本文引用的文献

1
Tinker 8: Software Tools for Molecular Design.Tinker 8:分子设计软件工具。
J Chem Theory Comput. 2018 Oct 9;14(10):5273-5289. doi: 10.1021/acs.jctc.8b00529. Epub 2018 Sep 19.
2
Geometry optimisations with a nonlocal density-functional theory method based on a double Hirshfeld partitioning.采用基于双 Hirshfeld 分区的非局域密度泛函理论方法进行几何优化。
J Chem Phys. 2018 Jul 28;149(4):044103. doi: 10.1063/1.5032175.
3
How important are dispersion interactions to the strength of aromatic stacking interactions in solution?
在溶液中,色散相互作用对芳香堆积相互作用的强度有多重要?
Chem Sci. 2015 Jul 1;6(7):4358-4364. doi: 10.1039/c5sc01370d. Epub 2015 May 18.
4
Intramolecular interactions in sterically crowded hydrocarbon molecules.空间拥挤烃分子中的分子内相互作用。
J Comput Chem. 2017 Nov 5;38(29):2500-2508. doi: 10.1002/jcc.24908. Epub 2017 Aug 7.
5
Symmetry-Adapted Perturbation Theory Energy Analysis of Alkyl Fluorine-Aromatic Interactions in Torsion Balance Systems.扭转平衡系统中烷基氟-芳香族相互作用的对称适配微扰理论能量分析
J Phys Chem A. 2016 Nov 23;120(46):9292-9298. doi: 10.1021/acs.jpca.6b09193. Epub 2016 Nov 10.
6
Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.用 AMOEBA 极化力场评估小分子的溶剂化自由能。
J Comput Chem. 2016 Dec 15;37(32):2749-2758. doi: 10.1002/jcc.24500. Epub 2016 Oct 19.
7
Advanced Potential Energy Surfaces for Molecular Simulation.用于分子模拟的高级势能面
J Phys Chem B. 2016 Sep 22;120(37):9811-32. doi: 10.1021/acs.jpcb.6b06414.
8
Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field.使用AMOEBA可极化力场评估水合自由能计算的参数化协议。
J Chem Theory Comput. 2016 Aug 9;12(8):3871-83. doi: 10.1021/acs.jctc.6b00276. Epub 2016 Jul 29.
9
Molecular energies from an incremental fragmentation method.基于增量碎裂法的分子能量
J Chem Phys. 2016 Feb 28;144(8):084109. doi: 10.1063/1.4942189.
10
Parameterization of the DFTB3 method for Br, Ca, Cl, F, I, K, and Na in organic and biological systems.用于有机和生物体系中溴、钙、氯、氟、碘、钾和钠的DFTB3方法的参数化
J Chem Theory Comput. 2015 Jan 13;11(1):332-42. doi: 10.1021/ct5009137.