在水性溶剂中二二子的形状偏好
Francisco Adasme-Carreño1,2, Alvaro Ochoa-Calle3, Marcelo Galván3
1Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectorá de Investigación y Postgrado Universidad Católica del Maule, Talca 3480112, Chile. fadasme@ucm.cl.
Physical chemistry chemical physics : PCCP
|February 22, 2024
概括
在溶液中准确建模zwitterions是很困难的. 密度函数理论与CANDLE溶解模型准确预测水中的二形状,匹配晶体结构.
科学领域:
- 计算化学是一种计算化学.
- 生物分子建模模型
- 物理化学 物理化学
背景情况:
- 准确的理论描述溶剂对zwitterions的影响,特别是在水环境中,仍然是一个重大挑战.
- 兹维特里克状态对于和蛋白质的结构和功能至关重要,但它们的溶解是复杂的模型.
- 在zwitterionic形式的疏水性二酸具有特殊的挑战,因为它们具有独特的电荷分布和与水的相互作用.
研究的目的:
- 评估各种理论方法的准确性,特别是密度函数理论 (DFT) 与不同的隐性溶剂模型,用于描述水溶液中的兹维特里昂.
- 通过使用验证的理论方法来确定十二种疏水性二在它们的zwitterionic状态中的首选溶解构造.
- 为了评估电荷不对称的非局部确定局部电解模型 (CANDLE) 与DFT一起用于建模zwipterionic dipeptides的性能.
主要方法:
- 验证DFT和隐性溶剂模型,使用在水溶剂中的实验性甘氨酸复合能量.
- 应用经过验证的DFT-CANDLE方法来探索十二个疏水性二二子的构造空间.
- 集成DFT计算 (真空和显式水) 和经典分子动力学模拟在显式溶剂中,以获得CANDLE-solvated结构.
主要成果:
- 电荷不对称的非局部确定局部电溶解模型 (CANDLE) 与DFT相结合,与实验性甘氨酸复合能量表现出极好的一致性.
- 通过使用DFT-CANDLE方法成功确定了研究的二二子的能量有利的构造.
- 预测的最稳定的溶解体构造非常类似于在各自的晶体结构中观察到的二二子的结构.
结论:
- DFT-CANDLE方法提供了对溶解的准确描述,克服了以前的理论限制.
- 预测的溶解结构和晶体结构之间的密切一致性表明,二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二二
- 这项研究验证了一种强大的计算策略,用于研究水性环境中zwipterionic的构造性行为.
更多相关视频
06:50Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
1.8K
05:45Capillary Electrophoresis-based Hydrogen/Deuterium Exchange for Conformational Characterization of Proteins with Top-down Mass Spectrometry
Published on: June 8, 2021
3.3K
相关概念视频
03:13Intermolecular Forces
58.3K
Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen...
58.3K
02:42Aqueous Solutions and Heats of Hydration
14.7K
Water and other polar molecules are attracted to ions. The electrostatic attraction between an ion and a molecule with a dipole is called an ion-dipole attraction. These attractions play an important role in the dissolution of ionic compounds in water.
When ionic compounds dissolve in water, the ions in the solid separate and disperse uniformly throughout the solution because water molecules surround and solvate the ions, reducing the strong electrostatic forces between them. This process...
When ionic compounds dissolve in water, the ions in the solid separate and disperse uniformly throughout the solution because water molecules surround and solvate the ions, reducing the strong electrostatic forces between them. This process...
14.7K
02:40Ligand Binding Sites
12.8K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.8K
02:34Regioselectivity and Stereochemistry of Acid-Catalyzed Hydration
8.4K
The rate of acid-catalyzed hydration of alkenes depends on the alkene's structure, as the presence of alkyl substituents at the double bond can significantly influence the rate.
8.4K
01:21Basicity of Aliphatic Amines
5.9K
Amines can behave as Brønsted–Lowry bases by accepting a proton from the acid to form corresponding conjugate acids. Due to a lone pair of nonbonding electrons, aliphatic amines can also act as Lewis bases by forming a covalent bond with an electrophile.
To measure the basicity of amines, two conventions are generally used. The first defines Kb as the basicity constant for the deprotonation reaction of water by the amine, as presented in Figure 1. Conventionally, lower Kb indicates...
To measure the basicity of amines, two conventions are generally used. The first defines Kb as the basicity constant for the deprotonation reaction of water by the amine, as presented in Figure 1. Conventionally, lower Kb indicates...
5.9K
01:16Titration in Nonaqueous Solvents
795
Most acid-base titrations are performed in an aqueous medium. In aqueous titrations, water competes with weaker acids or bases for proton donation or acceptance, leading to ambiguous endpoints in the titration curve. Water also affects the partial ionization of weak acids or bases. For example, water accepts a proton from acetic acid to form hydronium and acetate ions. The hydronium ion formed is a stronger acid than acetic acid, and the acetate ion is a stronger base than water. As a result,...
795