Vibrational mode frequencies of H4SiO4, D4SiO4, H6Si2O7, and H6Si3O9 in aqueous environment, obtained from ab initio molecular dynamics

2012 ◽  
Vol 137 (16) ◽  
pp. 164506 ◽  
Author(s):  
Georg Spiekermann ◽  
Matthew Steele-MacInnis ◽  
Piotr M. Kowalski ◽  
Christian Schmidt ◽  
Sandro Jahn
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Vibrational Mode ◽  
Ab Initio Molecular Dynamics ◽  
Aqueous Environment

scholarly journals Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics

Polymers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 3434
Author(s):  
Khagendra Baral ◽  
Puja Adhikari ◽  
Bahaa Jawad ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Molecular Dynamics ◽  
Body Temperature ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Rgd Peptide ◽  
Ab Initio Molecular Dynamics ◽  
Quantum Mechanical ◽  
Aqueous Environment ◽  
Structure And Properties

The structure and properties of the arginine-glycine-aspartate (RGD) sequence of the 1FUV peptide at 0 K and body temperature (310 K) are systematically investigated in a dry and aqueous environment using more accurate ab initio molecular dynamics and density functional theory calculations. The fundamental properties, such as electronic structure, interatomic bonding, partial charge distribution, and dielectric response function at 0 and 310 K are analyzed, comparing them in dry and solvated models. These accurate microscopic parameters determined from highly reliable quantum mechanical calculations are useful to define the range and strength of complex molecular interactions occurring between the RGD peptide and the integrin receptor. The in-depth bonding picture analyzed using a novel quantum mechanical metric, the total bond order (TBO), quantifies the role played by hydrogen bonds in the internal cohesion of the simulated structures. The TBO at 310 K decreases in the dry model but increases in the solvated model. These differences are small but extremely important in the context of conditions prevalent in the human body and relevant for health issues. Our results provide a new level of understanding of the structure and properties of the 1FUV peptide and help in advancing the study of RGD containing other peptides.

scholarly journals Vibrational mode frequencies of silica species in SiO2-H2O liquids and glasses from ab initio molecular dynamics

2012 ◽  
Vol 136 (15) ◽  
pp. 154501 ◽  
Author(s):  
Georg Spiekermann ◽  
Matthew Steele-MacInnis ◽  
Christian Schmidt ◽  
Sandro Jahn
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Vibrational Mode ◽  
Ab Initio Molecular Dynamics

Ab initio molecular dynamics investigation of structural, dynamic and spectroscopic aspects of Se(vi) species in the aqueous environment

2016 ◽  
Vol 18 (21) ◽  
pp. 14561-14568 ◽  
Author(s):  
Sangkha Borah ◽  
P. Padma Kumar
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Microscopic Investigation ◽  
Ab Initio Molecular Dynamics ◽  
Aqueous Environment ◽  
Structural Dynamic ◽  
Selenic Acid ◽  
Spectroscopic Signatures

Microscopic investigation of selenic acid in aqueous environment is carried out. Hydrogen bonding and spectroscopic signatures of HSeO4−and SeO42−species are discussed.

Ab initio molecular dynamics study of Se(iv) species in aqueous environment

2016 ◽  
Vol 18 (38) ◽  
pp. 26755-26763 ◽  
Author(s):  
Sangkha Borah ◽  
P. Padma Kumar
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Aqueous Environment ◽  
Water Borne

Anab initiomolecular dynamics investigation is carried out on various water-borne Se(iv) species, H2SeO3, HSeO3−and SeO32−, in aqueous environment.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

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.

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