Dissociation Constants of Weak Acids from ab Initio Molecular Dynamics Using Metadynamics: Influence of the Inductive Effect and Hydrogen Bonding on pKa Values

2014 ◽  
Vol 118 (47) ◽  
pp. 13651-13657 ◽  
Author(s):  
Anil Kumar Tummanapelli ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Inductive Effect ◽  
Dissociation Constants ◽  
Ab Initio Molecular Dynamics ◽  
Weak Acids ◽  
Pka Values

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study

2014 ◽  
Vol 16 (33) ◽  
pp. 17458-17465 ◽  
Author(s):  
Rajdeep Singh Payal ◽  
Sundaram Balasubramanian
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Simulation Study ◽  
Molecular Hydrogen ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

Dissolution of cellulose in ionic liquids involves breaking of its inter- and intra-molecular hydrogen bonding network, as seen through ab initio molecular dynamics simulations.

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.

Estimating successive pKa values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers

2015 ◽  
Vol 17 (9) ◽  
pp. 6383-6388 ◽  
Author(s):  
Anil Kumar Tummanapelli ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Phthalic Acid ◽  
Ab Initio Molecular Dynamics ◽  
Pka Values

pKa values of polyprotic acids estimated from ab initio molecular dynamics computation of the change in free energy upon dissociation.

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.

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