Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

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Structural and Molecular Dynamics Analysis of Plant Serotonin N ‐Acetyltransferase Reveal an Acid/Base‐Assisted Catalysis in Melatonin Biosynthesis

Angewandte Chemie ◽

10.1002/ange.202100992 ◽

2021 ◽

Author(s):

Lijing Liao ◽

Yuanze Zhou ◽

Youdong Xu ◽

Yuhao Zhang ◽

Xikai Liu ◽

...

Keyword(s):

Molecular Dynamics ◽

Dynamics Analysis ◽

Acid Base

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Antitumor drugs effect on the stability of double-stranded DNA: steered molecular dynamics analysis

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2021.1960193 ◽

2021 ◽

pp. 1-10

Author(s):

Rakesh Kumar Mishra ◽

Lakshmi Maganti

Keyword(s):

Molecular Dynamics ◽

Steered Molecular Dynamics ◽

Antitumor Drugs ◽

Dynamics Analysis ◽

Double Stranded Dna ◽

The Stability

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A Review on Combination of Ab Initio Molecular Dynamics and NMR Parameters Calculations

International Journal of Molecular Sciences ◽

10.3390/ijms22094378 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4378

Author(s):

Anna Helena Mazurek ◽

Łukasz Szeleszczuk ◽

Dariusz Maciej Pisklak

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Small Amplitude ◽

Ab Initio Molecular Dynamics ◽

Quantum Mechanical ◽

Time Step ◽

Noticeable Effect ◽

Nmr Parameters ◽

Mechanical Methods ◽

Simulation Time

This review focuses on a combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations using quantum mechanical methods. The advantages of such an approach in comparison to the commonly applied computations for the structures optimized at 0 K are presented. This article was designed as a convenient overview of the applied parameters such as the aiMD type, DFT functional, time step, or total simulation time, as well as examples of previously studied systems. From the analysis of the published works describing the applications of such combinations, it was concluded that including fast, small-amplitude motions through aiMD has a noticeable effect on the accuracy of NMR parameters calculations.

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