Name: isotopic effect in double proton transfer process of porphycene investigated by enhanced qm/mm method
Uploaded: 2019-07-19T15:00:00
Description: Watch this Scientific Journal Video about Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method at JoVE.com

本研究得到国家重点研究与发展计划(2017YFA0206801,2018YFA0208600),江苏省自然科学基金, 国家自然科学基金(91645116)的支持。L.X是江苏工业大学特聘教授。作者肯定了胡浩博士和杨明军博士的建议。

1. 建筑模型
<ol><li>
构建孔生结构:通过双击鼠标打开高斯视图软件。然后单击高斯视图菜单中的"元素片段"按钮以选择所需的元素。构造孔生。然后单击"文件"按钮以保存为 pdb 文件。</li>
	<li>
索尔瓦特模型:通过在 linux 操作系统中发出命令,在边缘长度为 38 Ω 的立方 TIP3P21水盒中,Solvate porphyc...

<ol>
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图1显示了紫金石的结构。用SITS方法的静电嵌入QM/MM混合电位来描述水中的化学反应23、24。质子转移发生在波生3内,因此,波生被设置为QM区域,提醒水被设置为MM区域。在这里,我们采用DFTB/MIO作为我们的QM方法,通过平衡效率和准确性22,25来治疗猪科。作为一种采样增强技术...

质子转移过程在分子开关、晶体管和信息存储装置1、2的开发中具有潜在的应用价值。特别是,通过双质子转移过程对光子的陶化引起了光谱学和光物理2领域的广泛关注。通过双质子转移过程,孔生的内部氢原子可以从一个转异体转移到另一个等效的转异体,如图1所示。 提出了双质子转移过程的两个机制:协同和逐步机制3,4。在协调的双质子转移过程中,两个质子原子以对称方式同步地移动到过渡状态,而一个质子在另一个质子之前以逐步过程完成转移。两个氢原子可以同时或逐步转移,这取决于两个氢原子之间的相关强度5。
同位素替代已用于检测分子的结构性质和反应动力学的速率常数6。单二元替代在猪的内氢导致分子的不对称形状。由于氢原子和铀原子之间的质量差异,氢键可能会膨胀或收缩。同位素替代在孔雀脚手架上引入扰动。问题是,不对称结构是否会影响质子转移过程。Limbach和同事报告说,用二氢替换氢将压缩两种氢键,而两个氢键在porphycene中的协同耦合可能有利于协同机制7,而吉川则指出去功能化将使逐步机制的贡献大于协同机制8。实验技术,如力谱,已经开发,以捕获在单个孔素9的陶化细节。然而,由于质子转移的瞬态性,要确定其原子细节仍然具有挑战性。
理论计算和模拟可以作为阐明质子转移反应机制的补充工具。在不同的理论方法中,分子动力学(MD)模拟可以监测每个原子的动态运动,并广泛用于揭示化学和酶反应的复杂机制。然而,定期的MD模拟往往受到采样不足的影响,特别是当在感兴趣的过程中存在高能量屏障时。因此,已经开发出了增强的采样方法,包括过渡路径采样10、11、伞式采样(美国)12、13和综合回火采样(ITS)14。 15.结合不同的增强采样方法,可进一步提高采样效率16、17、18。为了利用增强的采样算法模拟化学反应,我们最近19日采用了具有量子力学和分子力学(QM/MM)电位的选择性集成回火采样(SITS)方法。建议的SITS-QM/MM方法结合了两种方法的优点:SITS方法加速采样,并可以在事先了解反应机制的情况下探索所有可能的反应通道,而QM/MM则提供了更准确的描述。粘结形成和粘结断裂过程,不能单靠MM方法来模拟。已实施的SITS-QM/MM方法成功地在不同系统中发现了协同双质子转移、不相关和相关的双质子传递机制,没有预先确定反应坐标19。对于porphycene,有19个报告是分步但相关的质子转移特性。混合SITS-QM/MM方法用于研究本研究的泊生子中同位素效应,下面是该方法算法和协议的详细说明。
我们实现了具有混合 QM/MM 潜力的 SITS 方法。SITS 的有效电位被定义为包括不同温度下的电位能量,以及加权因子 n k,以覆盖更广泛的温度范围,
<img alt="Equation 1" src="/files/ftp_upload/60040/60040equ01.jpg">
其中,N是规范项的数量,α k是反向温度,n k是每个规范分量的相应权重因子。UE (R) 和UN(R) 表示 SITS 中的增强和非增强术语,定义为:
<img alt="Equation 2" src="/files/ftp_upload/60040/60040equ02.jpg">
Us、Ue和Ue是子系统的势能,是子系统与环境的相互作用,是环境的潜在能量。 QM/MM 电位表示为三个组件的混合总和,
<img alt="Equation 3" src="/files/ftp_upload/60040/60040equ03.jpg">
其中U qm、U qm/mm和U mm分别是QM子系统的内部能量术语、QM和MM区域之间的相互作用能量以及MM子系统内的相互作用能量。 Uqm/mm术语可进一步分为三个组分,包括静态、范德瓦尔斯和 QM 原子和 MM 原子之间的共价相互作用能量项,
<img alt="Equation 4" src="/files/ftp_upload/60040/60040equ04.jpg">
我们分配,并在 SITS 中分配<img alt="Equation 5" src="/files/ftp_upload/60040/60040equ05.jpg">到<img alt="Equation 6" src="/files/ftp_upload/60040/60040equ06.jpg">一个U术语中,
<img alt="Equation 7" src="/files/ftp_upload/60040/60040equ07.jpg">
然后,系统的全部电位被分解为子系统U的能量、子系统与环境Ue之间的相互作用能量以及环境Ue的能量。 例如,在目前的工作系统中,子系统是肺生,环境是水。
沿集合变量*(R) 的 PMF 配置文件派生为,
<img alt="Equation 8" src="/files/ftp_upload/60040/60040equ08.jpg">
N1+H1[ ] 每次氢传递的一般使用的反应坐标N2是q1 = (r1=r2)/2 和q2 = r1 = r2,其中是N1-H1的距离,r2是H1-N2.
该方法已在QM/MM MD仿真封装QM4D20中实现。完整的源代码和文档可在此处找到:http://www.qm4d.info/。
通常,SITS-QM/MM MD 仿真涉及四个步骤:预平衡(预坐);优化nk(选择坐);生产模拟和数据分析。

<table>
	<tbody>
		<tr>
			<td>operating system</td>
			<td>CentOS Linux release 6.0</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>QM4D software</td>
			<td>http://www.qm4d.info/</td>
			<td></td>
			<td>in-house program</td>
		</tr>
		<tr>
			<td>Computer desktop</td>
			<td>HP</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

isotopic effect in double proton transfer process of porphycene investigated by enhanced qm/mm method

猪体内的单一二元替代导致分子几何的不对称,可能影响紫杉醇分子的双质子转移过程。在这项研究中,我们应用了一种称为SITS-QM/MM的增强QM/MM方法,以研究氢/铀(H/D)同位素对双质子转移的影响。SITS-QM/MM分子动力学模拟中距离变化表明,该基图采用分步双质子转移机制。结构分析和双质子转移过程的自由能量转移表明,非对称同位素替代巧妙地压缩了共价氢键,并可能改变原来的过渡状态位置。

现行协议研究了单次转移对双质子转移过程的影响(图1)。检查了QM子系统和在预平衡和优化步骤中的水的电位能量,以确保能量已扩大到更广泛的能量范围(图2)。代表距离和角度变化(图3和图4),以及预测的自由能变化(图5)用于描述对几何和质子转移过程的替代效应。海豚。
<p class="jove_...

Watch this Scientific Journal Video about Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method at JoVE.com

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

本文提出了一种使用增强QM/MM方法研究双质子转移过程对双质子转移过程的同位素效应的协议。

增强QM/MM方法研究的植物双质子转移过程中的同位素效应

The single deuterium substitution in porphycene leads to an asymmetric molecular geometry, which may affect the double proton transfer process in the ...

增强型 QM/MM 方法克服了正常 QM/MM 仿真中的简单问题。六 QM/MM 方法可加速 QM 区域的选装配，并捕获化学反应通路，从而定义反应坐标。通过该协议，我们成功捕获了双质子转移的化学反应途径，揭示了对水中证明的转移机制的铀替代作用。该协议可用于探索卤素或我们的铀替代在药物的发现热鉴定。六QM/MM方法的主要优点是，在探索反应机制时，不需要它定义盐水反应坐标或引入化学反应通路装置。使我们能够识别可能的反应途径，在反应。该方法可采用并推广至高水平QM方法，可成为研究溶液中化学反应机制的重要工具。要开始此过程，请启动预设，将运行类型设置为 100，临时设置为 300，临时设置为 260，临时高度设置为 1300，在输入文件中步步为 120，000。然后，发出相应的命令，如下所示。在预设阶段，监视每个术语的能量以计算平均值。使用 grep Linux 命令提取能量。要修改 md 输入文件中的平均能量，请根据上一个命令行的输出计算平均能量，并修改输入文件中的 v 移位线以及新生成的平均值。通过键入命令以启动优化步骤，在 QM4D 程序中启动偏移。接下来，用宽限期程序插入能量传播，确保能量波动可以覆盖温度范围的最低端和最端。优化后，将偏移步骤的最终 nk 值保存到名为 nk 的新文件中。dat 在此协议中。若要准备 md 输入文件，请将 runtype 设置为新输入文件中的 runtype 以启动生产模拟步骤。将存储的 nk 文件指定文件名为 nkfile nk。在输入文件中的 dat。在目前系统中，时间步数设置为 6，400，000。仿真计数器取决于系统，因此可根据您的特定需求更改仿真统计。选择适当的时间步进，用于您自己的系统的不同状态之间的边际转换。通过发出相应的命令来启动 MD 模拟，在这些模拟中初始化生产。要监测生产阶段的粘结形成和断裂过程，请使用grep命令在模拟时间检查H1N1和H1N2的距离变化。对H2N3和H2N4也可以进行同样的操作。然后，在生产模拟期间使用累积距离值插入距离传播。从 GREp 命令生成的 QM4D 生成的生产输出文件中提取反应坐标和能量条件。将数据组织成四列，并在每个时间范围内将它们写入数据文件中。通过发出相应的命令来计算自由能量。最后，在二维景观上投射自由能量，键入相应的命令。本议定书研究了双质子转移过程的单一铀替代效应。对QM子系统的潜在能量以及预平衡和优化步骤中的水进行了检查，以确保QM区域的能量被扩展到更广泛的能量范围，而不受环境能量的影响。具有代表性的距离和角度变化，以及投影的自由能量变化，用于表征对孔生几何和质子转移过程的铀替代效应。六 QM/MM 方法实现了能源空间的增强装配。指定的合并范围应实现能源分布的扩大。该方法不仅捕获了可以传递的反应通道的顶部，而且具有识别反应机制导致的规范反应状态反应产品的潜力。该协议作为研究浓缩环境中化学反应机制的起点。更高级别的QM方法可以轻易地与六个QM/MM方法相结合，以探索未来更复杂的系统。

Research

JoVE Journal

Chemistry

High Precision Zinc Isotopic Measurements Applied to Mouse Organs

适用于鼠标机关高精度锌同位素测量

We present a procedure to measure with high precision zinc isotope ratios in mouse organs. Zinc is composed of 5 stable isotopes (64Zn, 66Zn, 67Zn, 68Zn ...

科研

化学

Layer-by-layer Synthesis and Transfer of Freestanding Conjugated Microporous Polymer Nanomembranes

层 - 层的合成和独立式共轭微孔聚合物纳米薄膜的转移

CMP as large surface area materials have attracted growing interest recently, due to their high variability in the incorporation of functional groups in ...

Synthesis and Exfoliation of Discotic Zirconium Phosphates to Obtain Colloidal Liquid Crystals

合成与盘状磷酸盐锆剥落获取胶体液晶

Due to their abundance in natural clay and potential applications in advanced materials, discotic nanoparticles are of interest to scientists and ...

Radiolabeling and Quantification of Cellular Levels of Phosphoinositides by High Performance Liquid Chromatography-coupled Flow Scintillation

放射性标记和磷酸肌醇的细胞水平的定量高效液相色谱耦合流动闪烁

Phosphoinositides (PtdInsPs) are essential signaling lipids responsible for recruiting specific effectors and conferring organelles with molecular ...

Characterization, Quantification and Compound-specific Isotopic Analysis of Pyrogenic Carbon Using Benzene Polycarboxylic Acids (BPCA)

Characterization, Quantification and Compound-specific Isotopic Analysis of Pyrogenic Carbon Using Benzene Polycarboxylic Acids BPCA

表征，气相炭用苯聚羧酸的定量和特定化合物同位素分析（BPCA）

Fire-derived, pyrogenic carbon (PyC), sometimes called black carbon (BC), is the carbonaceous solid residue of biomass and fossil fuel combustion, such as ...

Determination of Carbonyl Functional Groups in Bio-oils by Potentiometric Titration: The Faix Method

该Faix方法：生物油羰基官能团通过电位滴定法测定

Carbonyl compounds present in bio-oils are known to be responsible for bio-oil property changes upon storage and during upgrading. Specifically, carbonyls ...

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F&#8722;

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of FÃƒÆ’Ã‚Â¢Ãƒâ€¹Ã¢â‚¬Â '

由 F− 310 Nm 支队所示的阴离子光电子成像

Anion photoelectron imaging is a very efficient method for the study of energy states of bound negative ions, neutral species and interactions of unbound ...

Synthesis of Soft Polysiloxane-urea Elastomers for Intraocular Lens Application

软聚聚硅氧烷-尿素弹性体在人工晶体中的应用

This study discusses a synthesis route for soft polysiloxane-based urea (PSU) elastomers for their applications as accommodating intraocular lenses ...

Niobium Oxide Films Deposited by Reactive Sputtering: Effect of Oxygen Flow Rate

活性溅射沉积的氧化氮薄膜：氧气流速效应

Reactive sputtering is a versatile technique used to form compact films with excellent homogeneity. In addition, it allows easy control over deposition ...

Automated Sample Multiplexing by using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT)

Automated Sample Multiplexing by using Combined Precursor Isotopic Labeling and Isobaric Tagging cPILOT

使用组合前体同位素标签和同位素标记 （cPILOT） 实现自动样品多路复用

We have introduced a high throughput quantitative proteomics workflow, combined precursor isotopic labeling and isobaric tagging (cPILOT) capable of ...