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Mass Spectrometry: Molecular Fragmentation Overview

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can...

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

The fragmentation patterns observed for compounds such as carboxylic acids, esters, and amides in the mass spectra include ⍺-cleavage and McLafferty rearrangement. Fragmentation by ⍺-cleavage preferentially occurs at the carbon-carbon bond at the ⍺-position next to the carboxylic group to generate a neutral radical and a cation. Long chain compounds with hydrogen at their γ-carbon undergo McLafferty rearrangement to give a radical cation and a neutral alkene.
For example,...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Maxam-Gilbert Sequencing

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

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Updated: Jun 16, 2025

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

通过进化优化的自动分子碎片化.

Fiona C Y Yu¹, Jorge L Gálvez Vallejo¹, Giuseppe M J Barca²

¹School of Computing, Australian National University, Canberra, 2601, ACT, Australia.

Journal of cheminformatics

|August 19, 2024

概括

此摘要是机器生成的。

通过自动基因搜索快速碎片化 (QFRAGS) 是一种用于分子碎片化的新自动化算法. 它使用遗传优化来创建具有低能量误差的碎片,改进了大型分子的量子化学计算.

关键词:

碎片分子轨道的碎片.许多人体扩张.分子碎片化的分子碎片化分子图形理论分子图形理论量子化学计算量子化学计算

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科学领域:

计算化学的计算化学
量子化学是一个量子化学.
生物信息学是一种生物信息学.

背景情况:

分子碎片化减少了量子化学中的计算复杂性.
目前的碎片化方法缺乏自动化和强大的质量指标.
需要自动化方法在大型分子系统中进行实际应用.

研究的目的:

通过自动基因搜索 (QFRAGS) 引入快速碎片化,这是一种用于分子碎片化的新型自动化算法.
为多体扩展 (MBE) 开发一种生成分子碎片的算法,从而产生低能量错误.
为了提高大型量子化学的碎片化技术的自动化和准确性.

主要方法:

开发了QFRAGS,这是一个采用遗传优化程序的自动化碎片化算法.
使用MBE2和MBE3计算对蛋白质系统 (<500和>500个原子) 进行基准QFRAGS.
将QFRAGS与手动碎片化方案和碎片分子轨道 (FMO) 技术进行了比较.

主要成果:

在蛋白质系统上,QFRAGS实现了低的平均绝对能量误差 (MAEE):20.6 kJ/mol (MBE2,<500个原子),2.2 kJ/mol (MBE3,<500个原子),181.5 kJ/mol (MBE2,>500个原子) 和24.3 kJ/mol (MBE3,>500个原子).
在脂质甘油/甘油脂数据集上,QFRAGS产生了7.9kJ/mol (MBE2) 和0.3kJ/mol (MBE3) 的MAE.
在MAEE方面,QFRAGS表现出与手动碎片和FMO方法相比的或更高的性能.

结论:

QFRAGS有效地自动化了分子碎片化,产生高质量的碎片,能量误差最小.
该算法显著提高了对大型分子系统的量子化学计算的准确性和计算可行性.
QFRAGS代表了计算化学的实质性进步,使复杂的计算更容易获得.