scholarly journals Dissolution of Silk Fibroin in Mixtures of Ionic Liquids and Dimethyl Sulfoxide: On the Relative Importance of Temperature and Binary Solvent Composition

Polymers ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 13
Author(s):  
Omar A. El Seoud ◽  
Marc Kostag ◽  
Shirley Possidonio ◽  
Marcella T. Dignani ◽  
Paulo A. R. Pires ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Silk Fibroin ◽  
Regression Coefficients ◽  
Side Chain ◽  
Binary Solvent ◽  
Imidazolium Cation ◽  
Order Polynomial ◽  
Ether Oxygen ◽  
The Difference ◽  
Dynamics Simulations

We studied the dependence of dissolution of silk fibroin (SF) in mixtures of DMSO with ionic liquids (ILs) on the temperature (T = 40 to 80 °C) and DMSO mole fraction (χDMSO = 0.5 to 0.9). The ILs included BuMeImAcO, C3OMeImAcO, AlBzMe2NAcO, and Bu4NAcO; see the names and structures below. We used design of experiments (DOE) to determine the dependence of mass fraction of dissolved SF (SF-m%) on T and χDMSO. We successfully employed a second-order polynomial to fit the biopolymer dissolution data. The resulting regression coefficients showed that the dissolution of SF in BuMeImAcO-DMSO and C3OMeImAcO-DMSO is more sensitive to variation of T than of χDMSO; the inverse is observed for the quaternary ammonium ILs. Using BuMeImAcO, AlBzMe2NAcO, and molecular dynamics simulations, we attribute the difference in IL efficiency to stronger SF-IL hydrogen bonding with the former IL, which is coupled with the difference in the molecular volumes and the rigidity of the phenyl ring of the latter IL. The order of SF dissolution is BuMeImAcO-DMSO > C3OMeImAcO-DMSO; this was attributed to the formation of intramolecular H-bonding between the ether oxygen in the side chain of the latter IL and the relatively acidic hydrogens of the imidazolium cation. Using DOE, we were able to predict values of SF-m%; this is satisfactory and important because it results in economy of labor, time, and material.

scholarly journals Studies on the Antibacterial Influence of Two Ionic Liquids and their Corrosion Inhibition Performance

2020 ◽  
Vol 10 (4) ◽  
pp. 1444 ◽  
Author(s):  
Mohamed F. Shehata ◽  
Ashraf M. El-Shamy ◽  
Khaled M. Zohdy ◽  
El-Sayed M. Sherif ◽  
Sherif Zein El Abedin
Keyword(s):  
Ionic Liquid ◽  
Ionic Liquids ◽  
Synergistic Effect ◽  
Corrosion Inhibition ◽  
Hydroxyl Group ◽  
Side Chain ◽  
Imidazolium Cation ◽  
Corrosion Effect ◽  
Inhibition Performance

In this paper the anti-bacterial and the anti-corrosion effect of two different ionic liquids, namely 1-(2-hydroxyethyl)-3-methylimidazolinium chloride ([OH-EMIm]Cl) and 1-ethyl-3-methyleimidazolinium chloride ([EMIm]Cl) was demonstrated. The results revealed that the corrosion inhibition influence of the ionic liquid [OH-EMIm]Cl is higher than that of the ionic liquid [EMIm]Cl. Furthermore, the ionic liquid [OH-EMIm]Cl showed better biocidal influence compared with the ionic liquid [EMIm]Cl. This indicates the synergistic effect due to the incorporation of the hydroxyl group into the side chain of the imidazolium cation leading to enhanced antibacterial and anticorrosion effect.

Effects of the ether oxygen atom in alkyl side chains on the physical properties of piperidinium ionic liquids

2018 ◽  
Vol 206 ◽  
pp. 523-534 ◽  
Author(s):  
T. Nokami ◽  
T. Yamashita ◽  
T. Komura ◽  
N. Handa ◽  
M. Shimizu ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Nitrogen Atom ◽  
Oxygen Atom ◽  
Physical Properties ◽  
Side Chain ◽  
Alkyl Side Chain ◽  
Ether Oxygen Atom ◽  
Alkyl Side Chains ◽  
Ether Oxygen ◽  
Positively Charged

Various types of piperidinium ionic liquids equipped with an oxygen atom-containing alkyl side chain on the positively charged nitrogen atom were systematically synthesized and their physical properties investigated.

Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation

2020 ◽  
Author(s):  
Julian Keupp ◽  
Johannes P. Dürholt ◽  
Rochus Schmid
Keyword(s):  
First Principles ◽  
Good Accuracy ◽  
Field Investigation ◽  
Square Lattice ◽  
Side Chain ◽  
Second Step ◽  
Side Chains ◽  
Dynamics Simulations ◽  
Complex Phenomena ◽  
Closed Pore

The prototypical pillared layer MOFs, formed by a square lattice of paddle-<br>wheel units and connected by dinitrogen pillars, can undergo a breathing phase<br>transition by a “wine-rack” type motion of the square lattice. We studied this not<br>yet fully understood behavior using an accurate first principles parameterized force<br>field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc:<br>benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi-<br>cations for an interface between a closed and an open pore phase traveling through<br>the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In<br>conventional simulations in small supercells this mechanism is prevented by periodic<br>boundary conditions (PBC), enforcing a synchronous transformation of the entire<br>crystal. Here, we extend this investigation to pillared layer MOFs with flexible<br>side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen-<br>tally known to have different properties with the side-chains acting as fixed guest<br>molecules. First, in order to extend the parameterization for such flexible groups,<br>1a new parametrization strategy for MOF-FF had to be developed, using a multi-<br>structure force based fit method. The resulting parametrization for a library of<br>fu-MOFs is then validated with respect to a set of reference systems and shows very<br>good accuracy. In the second step, a series of fu-MOFs with increasing side-chain<br>length is studied with respect to the influence of the side-chains on the breathing<br>behavior. For small supercells in PBC a systematic trend of the closed pore volume<br>with the chain length is observed. However, for a nanocrystallite model a distinct<br>interface between a closed and an open pore phase is visible only for the short chain<br>length, whereas for longer chains the interface broadens and a nearly concerted trans-<br>formation is observed. Only by molecular dynamics simulations using accurate force<br>fields such complex phenomena can be studied on a molecular level.

Modeling the Effects of O-sulfonation on the CID of Serine

2020 ◽  
Author(s):  
Kenneth Lucas ◽  
George Barnes
Keyword(s):  
Sulfo Group ◽  
High Energy ◽  
Empirical Method ◽  
Side Chain ◽  
Energy Structure ◽  
Direct Dynamics ◽  
Theoretical Mass ◽  
Intermolecular Proton Transfer ◽  
Dynamics Simulations ◽  
Semi Empirical

We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of \textit{O}-sulfonation on the collision induced dissociation for serine. Towards this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems. Peaks related to the sulfo group are identified and the reaction dynamics explored. In particular, three significant peaks (m\z 106, 88, and 81) seen in the theoretical mass spectrum directly related to the sulfo group are analyzed as well as major peaks shared by both systems. Our analysis shows that the m\z 106 peaks result from intramolecular rearrangements, intermolecular proton transfer among complexes composed of initial fragmentation products, and at high energy side-chain fragmentation. The \mz 88 peak was found to contain multiple constitutional isomers, including a previously unconsidered, low energy structure. It was also seen that the RM1 semi empirical method was not able to obtain all of the major peaks seen in experiment for sulfoserine. In contrast, PM6 did obtain all major experimental peaks.

Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

2020 ◽  
Vol 16 (4) ◽  
pp. 451-459 ◽  
Author(s):  
Fortunatus C. Ezebuo ◽  
Ikemefuna C. Uzochukwu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Binding Energy ◽  
Binding Site ◽  
Conformational Dynamics ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Conformational Selection ◽  
Hybrid Mechanism ◽  
Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

Prediction of Ionic Liquids Properties through Molecular Dynamics Simulations

2014 ◽  
Vol 4 (2) ◽  
pp. 151-172 ◽  
Author(s):  
Marta L.S. Batista ◽  
Joao A.P. Coutinho ◽  
Jose R.B. Gomes
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations
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