Direct Simulations of Anharmonic Infrared Spectra Using Quantum Mechanical/Effective Fragment Potential Molecular Dynamics (QM/EFP-MD): Methanol in Water

2012 ◽  
Vol 116 (36) ◽  
pp. 8965-8971 ◽  
Author(s):  
Manik Kumer Ghosh ◽  
Jooyong Lee ◽  
Cheol Ho Choi ◽  
Minhaeng Cho
Keyword(s):  
Molecular Dynamics ◽  
Infrared Spectra ◽  
Quantum Mechanical ◽  
Effective Fragment Potential

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<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>

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

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.

Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations

2014 ◽  
Vol 10 (8) ◽  
pp. 3190-3199 ◽  
Author(s):  
David Semrouni ◽  
Ashwani Sharma ◽  
Jean-Pierre Dognon ◽  
Gilles Ohanessian ◽  
Carine Clavaguéra
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Infrared Spectra ◽  
Finite Temperature ◽  
Dynamics Simulations

Quantum mechanical simulations of near-infrared spectra of biomolecules – Long-chain fatty acids

NIR news ◽  
2018 ◽  
Vol 29 (6) ◽  
pp. 13-19 ◽  
Author(s):  
Krzysztof B Beć ◽  
Justyna Grabska
Keyword(s):  
Fatty Acids ◽  
Infrared Spectra ◽  
Near Infrared ◽  
Infrared Region ◽  
Quantum Mechanical ◽  
Long Chain Fatty Acids ◽  
Near Infrared Spectra ◽  
Technical Article ◽  
Long Chain ◽  
Chain Fatty Acids

Exact and in-depth interpretation of near-infrared spectra has often appeared problematic in any case stepping beyond the simplest molecules. The inherent complexity of near-infrared spectra due to the abundance of combination modes and the resulting extensive band overlay frequently limits our comprehension of the spectral bands to vague wavenumber regions in which certain modes likely appear. Coincidently, quantum mechanical simulation of spectra which could offer momentous support in solving such problems has rather been rare in the case of near-infrared region due to practical limitations. Recent years have seen a trending development of accurate and affordable methods of near-infrared spectra simulation. A trend in modelling increasingly complex molecules can be noticed reaching even fairly large biomolecules. In this technical article we overview the most recent accomplishments in the field on the example of long-chain fatty acids and their cyclic dimers, which extend beyond 100 atoms.

Sign in / Sign up

Export Citation Format

Share Document