Jove
Visualize
联系我们
JoVE
x logofacebook logolinkedin logoyoutube logo
关于 JoVE
概览领导团队博客JoVE 帮助中心
作者
出版流程编辑委员会范围与政策同行评审常见问题投稿
图书馆员
用户评价订阅访问资源图书馆顾问委员会常见问题
研究
JoVE JournalMethods CollectionsJoVE Encyclopedia of Experiments存档
教育
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab Manual教师资源中心教师网站
使用条款与条件
隐私政策
政策

相关概念视频

Fischer Projections02:18

Fischer Projections

13.0K
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines.
13.0K
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

26.1K
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
26.1K
Hückel's Rule Diagram of π MOs: Frost Circle01:08

Hückel's Rule Diagram of π MOs: Frost Circle

4.2K
The Frost circle or the inscribed polygon method is a graphical method for determining the relative energies of π molecular orbitals (MOs) for planar, fully conjugated, and monocyclic compounds. This method was first described by A. A. Frost and Boris Musulin in 1953.
A Frost circle is constructed by drawing a polygon whose number of edges is equal to the number of carbons of the given cyclic system, with one of the vertices pointing down. Then, a circle is drawn enclosing the polygon so...
4.2K
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

12.6K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
12.6K
Aromatic Hydrocarbon Cations: Structural Overview01:18

Aromatic Hydrocarbon Cations: Structural Overview

2.7K
Cycloheptatriene is a neutral monocyclic unsaturated hydrocarbon that consists of an odd number of carbon atoms and an intervening sp3 carbon in the ring. The three double bonds in the ring correspond to 6 π electrons, which is a Huckel number, and therefore satisfies the criteria of 4n + 2 π electrons. However, the intervening sp3 carbon disrupts the continuous overlap of p orbitals. As a result, cycloheptatriene is not aromatic.
Removing one hydrogen from the intervening CH2 group...
2.7K
Crystal Field Theory - Tetrahedral and Square Planar Complexes02:46

Crystal Field Theory - Tetrahedral and Square Planar Complexes

41.4K
Tetrahedral Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
41.4K

您也可能阅读

相关文章

通过共同作者、期刊和引用图与本文相关的文章。

排序
Same author

On the origins and variation of nucleotide skews of archaeal genomes.

Frontiers in microbiology·2026
Same author

The Nucleic Acids Circular Dichroism and Fourier Transform Databases NACDDB and NAIRDB: New Tools for RNA Structural Analysis.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

Application of Fourier Transform Infrared Spectroscopy for Structural Analysis of RNAs.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

Genome-wide ribonucleotide detection in Archaea.

Nucleic acids research·2025
Same author

Ultrafast photooxidation of semireduced flavin in fatty acid photodecarboxylase.

Science advances·2025
Same author

Editorial: The metabolic pathways of archaea.

Frontiers in microbiology·2025

相关实验视频

Updated: Jun 4, 2025

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.1K

添加式CHARMM力场用于氨酸和叶酸盐.

Elsa Balduzzi1, Wenlu Yin1, Jean-Christophe Lambry1

  • 1Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, Palaiseau, France.

Journal of computational chemistry
|December 22, 2024
PubMed
概括

这项研究开发了叶酸的新分子力学参数,对于单碳代谢至关重要. 优化的CHARMM36力场模型准确地模拟了不同氧化还原状态下的叶酸-蛋白相互作用.

关键词:
在CFFGenFF中使用.迷人的魅力叶酸是一种叶酸.实力场 实力场 实力场 实力场分子动力学分子动力学这就是Pterin pterin的意思.这是一种四水生物素 (tetrahydrobiopterin).甲基四基酸盐 (tetrahydrofolate) 是一种含有四基酸盐的化合物.

更多相关视频

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

5.6K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

317

相关实验视频

Last Updated: Jun 4, 2025

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.1K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

5.6K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

317

科学领域:

  • 生物化学和分子生物学
  • 计算化学的计算化学
  • 结构生物学 结构生物学

背景情况:

  • 叶酸是单碳代谢中必不可少的辅助因子,支持生物合成和表观遗传维护等关键生理过程.
  • 叶酸盐的氨酸环结构允许氧化还原反应和多个质子化状态,使分子建模复杂化.
  • 精确的分子力学 (MM) 参数是模拟生物系统中叶酸行为的必要条件.

研究的目的:

  • 导出和验证CHARMM36力场内的氨酸和生物相关叶酸的分子力学 (MM) 参数.
  • 开发18种不同叶酸的多重氧化还原状态 (氧化,二叶酸,四叶酸) 和质子化状态的参数.
  • 为了提高叶酸-蛋白相互作用的计算建模的准确性.

主要方法:

  • 使用CHARMM力场参数化协议来导出部分电荷和绑定项.
  • 采用量子力学计算,针对单水化合物相互作用,静电电位和电荷导数的二极 Moment.
  • 进行1D和2D潜在能量表面扫描,以参数化结合,角度和二面条,包括内环扭动.

主要成果:

  • 在CHARMM36力场中,成功对18种叶酸在各种还氧化和质子化状态进行了参数化.
  • 与初始参数相比,在蛋白质叶酸复合物的模拟中,优化叶酸模型的性能明显提高.
  • 新模型准确地复制了叶酸-蛋白相互作用的结构性质.

结论:

  • 开发的分子力学模型为模拟不同氧化还原状态中的叶酸提供了准确的参数.
  • 这个模型代表了计算研究涉及叶酸和叶酸衍生物的有价值的工具.
  • 优化的参数将推动单碳代谢和相关生物过程的研究.