Influence of Crystallization Additives on Morphology of Selected Benzoic Acids - A Molecular Dynamics (MD) Simulation Study

2021 ◽  
Vol 903 ◽  
pp. 22-27
Author(s):  
Aina Semjonova ◽  
Agris Bērziņš
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Md Simulation ◽  
Crystal Morphology ◽  
Hydroxybenzoic Acid ◽  
Benzoic Acids ◽  
Influence Of Crystallization ◽  
Polymorphic Forms ◽  
Model Substances ◽  
Dynamics Simulations

The possibility to modify the morphology by crystallization additives of model substances was studied using molecular dynamics simulations. For this 2,6-dimethoxybenzoic acid and 3-hydroxybenzoic acid, each having two polymorphic forms, including a form without carboxylic acid homodimers in their crystal structure were selected. For each polymorph 2-3 largest crystal faces were selected for the study and the crystal was cut along these planes by preparing a simulation box with these planes facing towards solution containing additives. In the performed study it was evaluated which additives potentially can influence the crystal morphology and possibly also polymorph obtained in the crystallization by significantly changing the growth rate of crystal by adsorbing on the surface. For the study 4-5 additives providing different intermolecular interaction possibilities were selected. Among the studied additives urea showed the most complete adsorption and the longest residence time on surfaces of both substances, with the exceptions of few specific planes.

scholarly journals Combined Use of Structure Analysis, Studies of Molecular Association in Solution, and Molecular Modelling to Understand the Different Propensities of Dihydroxybenzoic Acids to Form Solid Phases

Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 734
Author(s):  
Aija Trimdale ◽  
Anatoly Mishnev ◽  
Agris Bērziņš
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Molecular Association ◽  
Hydroxyl Groups ◽  
Solid Phases ◽  
Solvent Molecules ◽  
Dynamics Simulations

The arrangement of hydroxyl groups in the benzene ring has a significant effect on the propensity of dihydroxybenzoic acids (diOHBAs) to form different solid phases when crystallized from solution. All six diOHBAs were categorized into distinctive groups according to the solid phases obtained when crystallized from selected solvents. A combined study using crystal structure and molecule electrostatic potential surface analysis, as well as an exploration of molecular association in solution using spectroscopic methods and molecular dynamics simulations were used to determine the possible mechanism of how the location of the phenolic hydroxyl groups affect the diversity of solid phases formed by the diOHBAs. The crystal structure analysis showed that classical carboxylic acid homodimers and ring-like hydrogen bond motifs consisting of six diOHBA molecules are prominently present in almost all analyzed crystal structures. Both experimental spectroscopic investigations and molecular dynamics simulations indicated that the extent of intramolecular bonding between carboxyl and hydroxyl groups in solution has the most significant impact on the solid phases formed by the diOHBAs. Additionally, the extent of hydrogen bonding with solvent molecules and the mean lifetime of solute–solvent associates formed by diOHBAs and 2-propanol were also investigated.

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

scholarly journals Contributions of Molecular Dynamics Simulations to Elastohydrodynamic Lubrication

2021 ◽  
Vol 69 (1) ◽  
Author(s):  
James P. Ewen ◽  
Hugh A. Spikes ◽  
Daniele Dini
Keyword(s):  
Molecular Dynamics ◽  
Shear Rate ◽  
Experimental Design ◽  
Md Simulation ◽  
Elastohydrodynamic Lubrication ◽  
Quantitative Agreement ◽  
Coupling Methods ◽  
Fundamental Understanding ◽  
Shear Heating ◽  
Dynamics Simulations

AbstractThe prediction of friction under elastohydrodynamic lubrication (EHL) conditions remains one of the most important and controversial areas of tribology. This is mostly because the pressure and shear rate conditions inside EHL contacts are particularly severe, which complicates experimental design. Over the last decade, molecular dynamics (MD) simulation has played an increasingly significant role in our fundamental understanding of molecular behaviour under EHL conditions. In recent years, MD simulation has shown quantitative agreement with friction and viscosity results obtained experimentally, meaning that they can, either in isolation or through the use of multiscale coupling methods, begin to be used to test and inform macroscale models for EHL problems. This is particularly useful under conditions that are relevant inside machine components, but are difficult to obtain experimentally without uncontrollable shear heating.

Active site gate of M32 carboxypeptidases illuminated by crystal structure and molecular dynamics simulations

2017 ◽  
Vol 1865 (11) ◽  
pp. 1406-1415 ◽  
Author(s):  
Bhaskar Sharma ◽  
Sahayog N. Jamdar ◽  
Biplab Ghosh ◽  
Pooja Yadav ◽  
Ashwani Kumar ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamics Simulations

scholarly journals Predicting Melting Points of Biofriendly Choline-Based Ionic Liquids with Molecular Dynamics

2019 ◽  
Vol 9 (24) ◽  
pp. 5367 ◽  
Author(s):  
Karl Karu ◽  
Fred Elhi ◽  
Kaija Põhako-Esko ◽  
Vladislav Ivaništšev
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Melting Point ◽  
Chemical Space ◽  
Mean Square ◽  
Melting Points ◽  
Simulation Based ◽  
Predicted Values ◽  
Dynamics Simulations

In this work, we introduce a simulation-based method for predicting the melting point of ionic liquids without prior knowledge of their crystal structure. We run molecular dynamics simulations of biofriendly, choline cation-based ionic liquids and apply the method to predict their melting point. The root-mean-square error of the predicted values is below 24 K. We advocate that such precision is sufficient for designing ionic liquids with relatively low melting points. The workflow for simulations is available for everyone and can be adopted for any species from the wide chemical space of ionic liquids.

Molecular Dynamics Simulations of Liquid Crystalline Order for Tetramers of p-Hydroxybenzoic Acid

1994 ◽  
Vol 98 (31) ◽  
pp. 7685-7691 ◽  
Author(s):  
Johannes Huth ◽  
Thomas Mosell ◽  
Kai Nicklas ◽  
Alla Sariban ◽  
Juergen Brickmann
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Liquid Crystalline ◽  
Hydroxybenzoic Acid ◽  
Crystalline Order ◽  
Dynamics Simulations

Measuring the Spontaneous Curvature of Bilayer Membranes by Molecular Dynamics Simulations

2013 ◽  
Vol 13 (4) ◽  
pp. 1093-1106 ◽  
Author(s):  
Han Wang ◽  
Dan Hu ◽  
Pingwen Zhang
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Molecular Mechanisms ◽  
Bilayer Membrane ◽  
Spontaneous Curvature ◽  
Bilayer Membranes ◽  
Bead Diameter ◽  
The Mean ◽  
Dynamics Simulations ◽  
Theoretical Results

AbstractWe propose a mathematically rigorous method to measure the spontaneous curvature of a bilayer membrane by molecular dynamics (MD) simulation, which provides description of the molecular mechanisms that cause the spontaneous curvature. As a main result, for the membrane setup investigated, the spontaneous curvature is proved to be a constant plus twice the mean curvature of the membrane in its tensionless ground state. The spontaneous curvature due to the built-in transbilayer asymmetry of the membrane in terms of lipid shape is studied by the proposed method. A linear dependence of the spontaneous curvature with respect to the head-bead diameter difference and the lipid mixing ratio is discovered. The consistency with the theoretical results provides evidence supporting the validity of our method.

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