Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC

To understand how proteins function on a cellular level, it is of paramount importance to understand their structures and dynamics, including the conformational changes they undergo to carry out their function. For the aforementioned reasons, the study of large conformational changes in proteins has been an interest to researchers for years. However, since some proteins experience rapid and transient conformational changes, it is hard to experimentally capture the intermediate structures. Additionally, computational brute force methods are computationally intractable, which makes it impossible to find these pathways which require a search in a high-dimensional, complex space. In our previous work, we implemented a hybrid algorithm that combines Monte-Carlo (MC) sampling and RRT*, a version of the Rapidly Exploring Random Trees (RRT) robotics-based method, to make the conformational exploration more accurate and efficient, and produce smooth conformational pathways. In this work, we integrated the rigidity analysis of proteins into our algorithm to guide the search to explore flexible regions. We demonstrate that rigidity analysis dramatically reduces the run time and accelerates convergence.     

QCMS2 as a new method for providing insight into peptide fragmentation: The influence of the side‐chain and inter–side‐chain interactions

The identification of peptides and proteins from tandem mass spectra is a difficult task and multiple tools have been developed to aid this identification. We present a new method called quantum chemical mass spectrometry for materials science (QCMS²), which is based on quantum chemical calculations of bond orders, reaction, and transition‐state energies at the DFT/B3LYP/6‐311+G* level of theory. The method was used to describe the fragmentation pathways of five X‐His‐Ser tripeptides with X = Asn, Asp, Glu, Ser, and Trp, thereby focusing on the influence of the side chain and inter–side‐chain interactions on the fragmentation. The main features in the mass spectra of the five tripeptides were correctly reproduced, and a number of fragments were assigned to fragmentations involving the side chain and the influence of inter–side‐chain interactions. Product ion spectra were recorded to evaluate the capabilities and limitations of QCMS² and a number of conventional tools.     

Substituent effects on the isomerization of hydrazone switches driven by the intramolecular hydrogen bond

In this work, the substituent effects on hydrogen bonding in one kind of hydrazone-based switch are revealed. The E/Z isomerization ratios of these hydrazones and their intramolecular hydrogen bond strengths in the Z form were evaluated using NMR technique. Linear correlations between these parameters and Hammett empirical values for substituent effects are explored as well.     

Emergent Self-Assembly Pathways to Multidimensional Hierarchical Assemblies using a Hetero-Seeding Approach

The controlled formation of complex and functional 1-, 2-, and 3D hierarchical assemblies from molecular building blocks represents a key current challenge. Herein, we report the use of a seeded growth approach for a series of perylenediimide-based molecules (PDIs 1 – 4 ) to access otherwise inaccessible self-assembly pathways that yield complex hierarchical structures. The key to the new approach is to use hetero-seeds which possess a different composition and morphology from that of the molecular building block. For example, a nanotube seed (from PDI 3 ) and a microribbon seed (from PDI 4 ) were found to initiate different self-assembly pathways for PDI 1 , which normally assembles to yield nanocoils. This led to the formation of unprecedented 3D scroll-like and scarf-like hierarchical nanostructures, respectively. Also, the hetero-seeds from PDI 3 initiate hidden self-assembly pathways of PDI 2 to generate 1D tubular heterojunctions. Significantly, this new strategy offers new opportunities to create emergent and functional hierarchical and complex structures from small molecule precursors.     

快原子轰击(FAB)离子化法测定头孢拉定的质谱及其裂解途径的解析

头孢拉定(Cefradine)是第一代合成头孢类抗生素药,也是目前最常用的抗生素之一。有胶囊、片剂也有注射针剂。具有广谱的抗菌性能,由于它对革兰氏阳性及阴性杆菌敏感,故对治疗呼吸道感染颇有效,用途广、用量大,属于高效的头孢菌素。国内不少药厂都有研制,为此,我们对其质谱行为进行了分析。头孢拉定,化学名(6R,7R-[(R)-2-氨基-2-(1,4-环己烯基)乙酰氨基]-3-甲基-8-氧代-5-硫杂-1-氮杂双环[4.2.0】辛-2-烯-2-羧酸,其产品为一水化物。分子式C16H19N3O4S·H2O,结构见图1。     

二氢香芹酮的合成及其谱学研究

本文自留兰香油出发，合成了二氢香芹酮，经Ｈ＾１ＮＭＲ与Ｃ＾１３ＮＭＲ研究，并没有发生二氢香芹酮的异构化。     

Strategies for modelling of catalysts

Summary and conclusions The strategy summarised above in which modelling calculations are combined with QM cluster calculations is a viable procedure for the study of catalysis. Our discussion has emphasised studies of zeolite catalysts but the same approach could be used in modelling reactions catalysed on metal and metal oxide surfaces. Moreover, the techniques and potentials are available for these methods to have a wide range of applications.     

光异构化反应速率的量子理论

光异构化反应是在光场存在下，分子吸收光子引起的单分子化学反应，包括通常的异构化与环合、开环反应．一些作者用量子化学方法及分子轨道相关图和态相关图等方法对这类反应进行过研究［1］．本文用多声子光跃迁理论［2］研究光异构化反应，导出反应速率及其在低温条件下的解析表达式，对所得结果进行了讨论．1理论方法与结果在光异构化反应中，分子的电子状态与构型都发生变化，而且电子态的变化是与构型的改变紧密耦合的．分子的构型用分子的振动波函数来描写．由于电子与原子质量相差悬殊，可以采用绝热近似处理这一电子－振动相互作用…     

C_6H_2(OH)_3CH_3氧化成羟基苯甲酸反应路径的DFT研究

运用密度泛函(DFT)理论,采用Materials Studio 8.0,用GGA/BP方法研究了C_6H_2(OH)_3CH_3氧化成羟基苯甲酸的反应路径。结果表明,甲基上的氢原子被氧化成羟基以及羟基被氧化为醛基及醛基被氧化成羧基均为放热过程。分子C_6H_2(OH)_3CH_3中甲基氧化成羧基的主路径为三个氢原子氧化反应路径,其路径为C_6H_2(OH)_3CH_3+3O→C6H2(OH)3C(OH)3→C6H2(OH)3COOH+H2O,该路径受限于羟基直接被氧化成羧基过程,需克服130 k J/mol的反应势垒,反应速率常数对数ln(k)为-22.96 s-1;醛基、羟基优先被氧化成羧基的顺序为:-CHO-C(OH)3-HC(OH)2-H2C(OH);提高反应温度、氧气浓度均有利于羟基苯甲酸的生成,适当的催化剂有利于促进整个反应的进行。     

Ni-MoOx催化剂上的庚烷异构化

在常压固定床流动体系中研究了Ni-MoOx催化剂对正庚烷异构化反应的催化性能.将质量分数为2%～5%的Ni掺杂于MoO3中可有效地缩短催化剂的还原活化时间,并较大幅度地提高催化剂的比活性.Ni-MoOx催化剂上的正庚烷异构化的反应活化能为35.3kJ/mol,显著低于MoOx催化剂上的活化能(49.3kJ/mol),仅为双功能分子筛催化剂的1/3～1/4.